AWS Control Tower vs AWS Organizations isn't an either/or choice. Control Tower is built ON TOP of Organizations and literally cannot run without it. Yet most comparisons miss this fundamental relationship and fail to address a critical tradeoff: Control Tower is console-driven (clickops), while Organizations can be managed entirely through infrastructure-as-code.
This guide clarifies the hierarchical relationship between these services, provides a clear decision framework (including IaC alternatives to Control Tower), and breaks down the real costs involved. By the end, you'll understand exactly which approach fits your organization's governance needs and engineering culture.
Quick Comparison: What's the Fundamental Difference?
Here's the core relationship most comparisons miss: AWS Control Tower requires AWS Organizations as its foundation. You cannot deploy Control Tower without Organizations. Control Tower doesn't replace Organizations; it orchestrates Organizations alongside other AWS services (Config, CloudTrail, IAM Identity Center, Service Catalog) to create an automated landing zone.
Think of Organizations as building blocks: complete flexibility, manual assembly required. Think of Control Tower as a pre-fabricated house built with those blocks: faster setup, opinionated design, but you're working within the framework's constraints.
The reality for most organizations: If you use Control Tower, you're also using Organizations. The question isn't which to choose but whether you need the Control Tower layer on top.
The Hierarchical Relationship Explained
The architecture is straightforward once you understand the dependency:
- AWS Organizations (Foundation Layer): Provides account management primitives, organizational structure (root, OUs, accounts), and policy framework (SCPs, RCPs, declarative policies)
- AWS Control Tower (Orchestration Layer): Automates configuration of Organizations alongside other AWS services to create a governed landing zone
Both services share the same management account. Control Tower creates and manages resources within the Organizations structure. You always have direct access to Organizations capabilities even when using Control Tower.
This means you can create additional OUs outside Control Tower's governance, implement custom SCPs beyond Control Tower's controls, and use Organizations' newer policy types (RCPs, declarative policies) alongside Control Tower's managed controls.
Side-by-Side Feature Comparison
| Feature | AWS Organizations | AWS Control Tower |
|---|---|---|
| Purpose | Account management and policy framework | Automated landing zone with governance |
| Setup Time | Variable (manual configuration) | Less than 1 hour (automated) |
| Dependency | Standalone service | Requires Organizations |
| Dashboard | None built-in | Centralized compliance view |
| Controls | Manual SCPs/RCPs/policies | 750+ pre-built controls |
| Account Provisioning | CreateAccount API | Account Factory with templates |
| Drift Detection | None | Automated daily scanning |
| Compliance Mapping | Manual | 17+ frameworks mapped |
| Management Model | Console, CLI, or IaC | Primarily console (clickops) |
The key insight: Organizations is pure infrastructure. Control Tower is infrastructure plus orchestration plus opinions. Those opinions accelerate setup but constrain flexibility.
Understanding AWS Organizations
AWS Organizations provides the foundational layer for all multi-account strategies. Without Organizations, you can't implement Service Control Policies, consolidated billing, or any advanced governance features. For complete setup and implementation guidance including policy types, service integrations, and OU architecture, see our AWS Organizations: Complete Implementation Guide. For production configuration best practices, see AWS Organizations Best Practices.
Core Capabilities and Features
Consolidated Billing: A single bill for all accounts with volume discounts, Reserved Instance sharing, and Savings Plans benefits across the organization.
Account Management: Create accounts via the CreateAccount API, invite external accounts, and organize accounts into a hierarchical structure.
Organizational Units (OUs): Logical grouping of accounts up to 5 levels deep. OUs enable policy inheritance where controls applied to parent OUs cascade down to all member accounts.
Service Integration: Over 30 AWS services integrate with Organizations including Security Hub, GuardDuty, IAM Identity Center, and AWS Config. You can enable these services organization-wide with delegated administration.
Policy Types:
- Service Control Policies (SCPs): Permission guardrails defining maximum available permissions for IAM principals
- Resource Control Policies (RCPs): Control what principals (internal or external) can access resources
- Declarative Policies: Enforce configuration standards for EC2, VPC, and EBS
- Management Policies: Backup policies, tag policies, AI opt-out policies
Service Control Policies (SCPs) and Authorization
SCPs are the most powerful governance tool in Organizations. They define the maximum permissions that can be granted to IAM principals in member accounts. SCPs don't grant permissions; they filter what permissions IAM policies can provide.
Key characteristics:
- SCPs do not affect the management account (a critical security consideration)
- Maximum 5 SCPs per entity (root, OU, or account)
- Maximum 5,120 characters per policy
- Support full IAM policy language including conditions with Allow statements (as of 2024)
For practical implementation patterns, see our collection of production-ready SCP examples organized by organizational unit type.
When Organizations Alone Is Sufficient
Choose Organizations without Control Tower when:
- Maximum customization required: You need complete control without prescriptive constraints
- Existing complex architecture: You have a well-established custom environment that doesn't align with Control Tower's model
- Minimal compliance requirements: Basic SCPs are sufficient without extensive continuous monitoring
- Simple use cases: Small number of accounts (5-10) with straightforward governance needs
- Infrastructure-as-code priority: You want to manage all governance through code, not console clicks
Organizations-only requires deep AWS expertise and ongoing manual maintenance, but it provides complete architectural freedom.
Understanding AWS Control Tower
AWS Control Tower orchestrates multiple AWS services to automate the setup of a secure, compliant multi-account environment. It builds on Organizations to provide a prescriptive landing zone with pre-configured best practices.
For complete documentation, see the AWS Control Tower User Guide.
Landing Zone Architecture
When you set up Control Tower, it automatically creates:
Foundational Organizational Units:
- Security OU (mandatory): Contains log archive and audit accounts
- Additional OUs you configure for workloads
Shared Accounts:
- Management Account: Organizations management, billing, Control Tower administration
- Log Archive Account: Centralized repository for CloudTrail and Config logs
- Audit Account: Read-only access across accounts for security teams
Baseline Resources:
- Organization-level CloudTrail trail (v3.0+)
- AWS Config configurations in all enrolled accounts
- IAM Identity Center for centralized access
- Service Catalog products for account provisioning
Configuration Choices (some immutable after setup):
- Home Region (cannot be changed)
- Governed Regions
- VPC CIDR ranges (cannot be changed)
- KMS encryption settings
Controls and Governance (Preventive, Detective, Proactive)
Control Tower implements three types of controls:
Preventive Controls: Implemented using SCPs, RCPs, and declarative policies. They block non-compliant actions before they happen. Example: Preventing S3 bucket public access.
Detective Controls: Implemented using AWS Config rules. They detect violations after resources are created and surface them in the dashboard. Example: Detecting unencrypted EBS volumes.
Proactive Controls: Implemented using CloudFormation hooks. They validate IaC templates before deployment. Example: Requiring approved AMIs for EC2 instances.
Control Tower provides over 750 managed controls mapped to 17+ compliance frameworks (PCI-DSS, HIPAA, SOC 2, NIST, CIS Benchmarks). You can browse, filter, and enable controls with a single click.
Recent enhancements (2024-2025):
- Declarative policy-based controls for EC2, VPC, EBS
- Configurable RCPs with exemption capabilities
- 176 Security Hub controls integration
- Support for seven new compliance frameworks
Account Factory and Automation
Account Factory standardizes account creation through templates:
- Standardized Provisioning: Accounts created with consistent baselines (IAM Identity Center assignments, OU placement, VPC config, enabled controls)
- Service Catalog Integration: Built on Service Catalog provisioned products for programmatic access
- Account Factory for Terraform (AFT): Terraform-based customization with Git workflows and CI/CD integration
- Concurrent Provisioning: Up to 5 accounts provisioned simultaneously
Account enrollment applies Control Tower governance to existing accounts. Prerequisites include the AWSControlTowerExecution role and removal of existing AWS Config recorders.
The Clickops Tradeoff
Here's the critical issue most comparisons avoid: Control Tower is fundamentally console-driven.
While you can enable some controls via APIs or CloudFormation, the core Control Tower operations happen through the AWS Console:
- Landing zone setup and updates
- OU registration
- Account enrollment
- Drift repair
- Many control configurations
Why this matters for engineering teams:
- No version control: Changes made through the console aren't tracked in Git
- No pull request workflows: Governance changes bypass code review processes
- No automated testing: You can't test policy changes in a CI/CD pipeline before deployment
- Drift risk: Manual console changes create configuration drift that's difficult to track
- Reproducibility: You can't reliably recreate the landing zone from code
Account Factory for Terraform (AFT) provides partial IaC capability for account provisioning, but core Control Tower operations remain console-based. This clickops model conflicts with modern DevOps practices where infrastructure changes flow through version-controlled pipelines.
For teams that prioritize infrastructure-as-code, this tradeoff is often a dealbreaker.
Key Differences: Organizations vs Control Tower
Understanding the specific tradeoffs helps you make an informed decision.
Automation and Setup Complexity
AWS Organizations:
- Manual OU creation, manual policy writing, manual CloudTrail/Config setup
- Requires deep AWS expertise
- Timeline: Weeks to months for custom implementation
- Full control over every configuration decision
AWS Control Tower:
- One-click landing zone deployment in under 1 hour
- Guided setup wizard with prescriptive defaults
- Automated baseline resources and drift detection
- Limited customization during initial setup
The tradeoff: Speed and automation vs complete customization control.
Governance and Compliance Capabilities
AWS Organizations Governance:
- Manual SCP/RCP/declarative policy creation
- No built-in detective controls (requires manual Config setup)
- No compliance framework mapping
- Complete flexibility in policy design
- Full IaC support through CDK, Terraform, CloudFormation
AWS Control Tower Governance:
- 750+ pre-built controls (preventive, detective, proactive)
- Automatic mapping to 17+ compliance frameworks
- Centralized dashboard with compliance status
- One-click control enablement
- Limited IaC support (primarily console-driven)
The tradeoff: Build-your-own vs managed controls library, with IaC flexibility vs console convenience.
Account Management and Provisioning
AWS Organizations:
- CreateAccount API or console invitation
- Manual baseline configuration per account
- No standardized templates
- Full control over account configuration
AWS Control Tower:
- Account Factory with configurable templates
- Automated baseline deployment (Config, CloudTrail, IAM roles)
- Service Catalog integration for self-service
- Account Factory for Terraform (AFT) for advanced customization
The tradeoff: Manual control vs standardized automation.
Logging, Monitoring, and Visibility
AWS Organizations:
- No built-in dashboard
- Manual CloudTrail/Config setup per account
- Custom tooling required for compliance visibility
- Variable costs based on what you enable
AWS Control Tower:
- Automated organization-level CloudTrail (v3.0+)
- AWS Config deployed automatically with aggregator
- Pre-configured audit account with cross-account access
- Centralized compliance dashboard
- Automatic cost from Config/CloudTrail enablement
The tradeoff: Custom tooling vs out-of-box visibility, with associated cost implications.
Flexibility vs Prescriptive Best Practices
AWS Organizations Flexibility:
- Any OU structure design
- No naming conventions required
- No mandatory services or resources
- Full control over all configurations
AWS Control Tower Prescriptive Approach:
- Mandatory Security OU with specific accounts
- Recommended OU structure (extensible)
- Immutable choices after setup (home Region, VPC CIDR)
- Required baseline resources (CloudTrail, Config, IAM Identity Center)
Control Tower is opinionated but extensible. You can create OUs outside Control Tower structure, add custom SCPs via Organizations, and use the controls-dedicated experience (v4.0) for more flexibility without the full landing zone.
Which Should You Use? Decision Framework
The right approach depends on your organization's size, expertise, compliance needs, and engineering culture, particularly your preference for console-driven vs code-driven governance.
Use AWS Organizations Alone When:
- Infrastructure-as-code is non-negotiable: Your team manages all infrastructure through code and won't accept console-driven governance
- Maximum customization required: You need complete control without prescriptive constraints
- Existing complex architecture: You have a well-established environment that doesn't fit Control Tower's model
- Minimal compliance requirements: Basic SCPs are sufficient without extensive monitoring
- Simple use cases: Small number of accounts with straightforward needs
- Deep AWS expertise available: Your team can design and maintain custom multi-account architecture
Real-world example: A 10-person engineering team with 8 accounts, strong CDK expertise, and preference for GitOps workflows. They manage SCPs through CDK, deploy baselines via CloudFormation StackSets, and avoid Control Tower's console dependency entirely.
Use AWS Control Tower When:
- Rapid setup required: You need a governed environment in hours, not weeks
- Following AWS best practices: You want prescriptive guidance without custom design
- Compliance focus: You require extensive guardrails and audit capabilities from day one
- Limited AWS expertise: Your team lacks deep experience designing multi-account architectures
- Standardization priority: You need consistent baselines across all accounts
- Dashboard visibility: You want centralized compliance status without custom tooling
- Growing organization: You expect significant account growth and want automated governance
- Console-based workflows acceptable: Your team is comfortable with clickops for governance
Real-world example: A 50-person company with SOC 2 requirements, limited cloud engineering resources, and a need to demonstrate governance to customers quickly. Control Tower's pre-built controls and compliance dashboard provide immediate value despite the clickops tradeoff.
Consider IaC Alternatives to Control Tower
For teams committed to infrastructure-as-code, Control Tower's console-driven nature is often a dealbreaker. But you don't have to choose between Control Tower and building everything from scratch.
IaC-first alternatives that work directly with AWS Organizations:
CDK Landing Zone: Build landing zones using native AWS CDK with full version control. No framework abstraction, no proprietary configuration files. CloudFormation StackSets handle cross-account deployment automatically.
OrgFormation: Infrastructure-as-code specifically designed for AWS Organizations. Custom CLI but provides Organizations-native automation without Control Tower dependency.
Landing Zone Accelerator (LZA): AWS solution deployed via CloudFormation/CDK. More IaC-native than Control Tower but uses configuration-driven approach with significant complexity.
Why IaC alternatives are often better for DevOps-mature teams:
- Full version control and audit trail for all changes
- Pull request workflows for governance changes
- Automated testing of policy changes before deployment
- No drift from manual console changes
- Easier to replicate across environments
All these alternatives work directly with AWS Organizations, proving that Organizations is the true foundation while Control Tower is just one (console-driven) option for building on that foundation.
For a detailed comparison of these alternatives with implementation guidance, see our comprehensive guide: AWS Control Tower Alternatives: From Console to Code.
Decision Matrix by Organization Size and Preferences
| Factor | Organizations + IaC | Control Tower |
|---|---|---|
| Account Count: 1-10 | Suitable (simple governance) | Suitable if compliance needed |
| Account Count: 10-50 | Suitable with strong team | Recommended for most |
| Account Count: 50+ | Suitable with automation | Strongly recommended |
| Team: IaC/GitOps culture | Strongly preferred | May cause friction |
| Team: Console-comfortable | Unnecessary complexity | Good fit |
| Compliance: None/Basic | Sufficient | Overkill |
| Compliance: Moderate (1-2 frameworks) | Possible but manual | Strongly recommended |
| Compliance: Strict (multiple frameworks) | Complex manual implementation | Required |
| Timeline: Days | Not feasible | Only option |
| Timeline: Weeks | Feasible with expertise | Faster |
How Control Tower and Organizations Work Together
Understanding the technical integration helps you customize effectively and avoid conflicts.
The Complementary Relationship
Control Tower is architecturally dependent on Organizations. The integration works through several mechanisms:
Shared Management Account: Both services operate from the same Organizations management account. You don't maintain separate administrative contexts.
Unified Account Structure: Control Tower-created OUs and accounts exist within the Organizations hierarchy. Moving to Control Tower doesn't require restructuring.
Governance Scope:
- Control Tower governance applies only to registered OUs and enrolled accounts
- Organizations governance (SCPs, RCPs, declarative policies) applies to the entire organization
- This allows parallel operation of Control Tower-governed and non-governed accounts
Policy Evaluation: Both Control Tower-managed and custom Organizations policies evaluate together hierarchically. An action must be allowed by both to succeed.
What Control Tower Requires from Organizations
AWS Control Tower is closely associated with AWS Organizations. Understanding their integration is critical to avoid breaking your landing zone. For complete guidance, see the official AWS Control Tower and Organizations guidance.
Trusted Access: Control Tower requires trusted access enabled for controltower.amazonaws.com. This allows Control Tower to create OUs, move accounts, and attach SCPs. Never use the AWS Organizations DisableAWSServiceAccess API to turn off Control Tower service access. Doing so breaks drift detection features that guarantee accurate compliance reporting.
Service-Linked Roles: Control Tower creates AWSControlTowerExecution and other roles in enrolled accounts. These are protected by SCPs to prevent deletion.
The FullAWSAccess SCP Requirement: The FullAWSAccess SCP must remain attached and should not be merged with other SCPs. While changes to this SCP aren't reported as drift, modifications may affect Control Tower functionality in unpredictable ways. For example, if detached or modified, accounts may lose access to AWS Config recorders or create gaps in CloudTrail logging.
Permission Model Differences: Control Tower handles permission filtering differently than Organizations. If accounts are provisioned via Account Factory, end-users can see names and parents of all OUs in the Control Tower console, even without permission to retrieve them from Organizations directly. Control Tower doesn't support mixed permissions on organizations and administrators are expected to have full permissions.
What Happens When You Make Manual Changes in Organizations
This is where most teams run into trouble. Manual changes in AWS Organizations when Control Tower is installed cause drift or go untracked entirely.
Modifying Control Tower SCPs (Don't Do This):
- Do NOT update existing SCPs attached to an OU registered with Control Tower
- Doing so results in controls entering an unknown state
- Recovery requires resetting your landing zone or re-registering the OU
- Instead: Create new SCPs in Organizations and attach them to OUs separately, rather than editing SCPs that Control Tower created
Moving Accounts (Causes Drift):
- Moving already enrolled accounts into Control Tower from outside a registered OU causes drift that must be resolved manually
- If you use Organizations to move an OU into an organization created by Control Tower, the external OU is not registered
Creating or Inviting Accounts (Not Tracked):
- If you use Organizations to create, invite, or move accounts within a Control Tower organization, those accounts are NOT enrolled by Control Tower
- These changes are not recorded by Control Tower
- You'll need to enroll these accounts separately if you want Control Tower governance
The Core Problem: Control Tower expects to be the source of truth for governance changes. When you bypass it through Organizations directly, you create a split-brain scenario where Organizations reflects one state and Control Tower reflects another.
Extending Control Tower with Custom Organizations Policies
You CAN safely add custom policies beyond Control Tower, but you must follow specific rules:
Safe Operations:
- Create NEW SCPs: Add new SCPs in Organizations for requirements not covered by Control Tower—just don't edit Control Tower's SCPs
- Resource Control Policies: Use RCPs for data perimeter implementation
- Declarative Policies: Enforce EC2/VPC/EBS configurations beyond Control Tower controls
- Management Policies: Add backup policies, tag policies at organization level
Unsafe Operations (Will Cause Problems):
- Editing any SCP that Control Tower created
- Detaching or modifying the
FullAWSAccessSCP - Disabling trusted access for Control Tower
- Moving enrolled accounts between OUs via Organizations console
- Deleting Control Tower-managed resources (IAM roles, S3 buckets, SNS topics)
Best practice: Use Control Tower for baseline governance. Extend with new Organizations policies for organization-wide or advanced requirements. Never modify what Control Tower created—always create new policies alongside them.
Common Challenges with Control Tower
Before choosing Control Tower, understand the operational challenges you'll face.
Control Tower Drift and Management Overhead
Drift is inevitable with Control Tower's console-driven model. Any manual change outside Control Tower causes drift:
- Modifying SCPs in Organizations console
- Moving accounts between OUs via Organizations
- Changing CloudTrail or Config configurations directly
Drift resolution is manual. You must use the Control Tower console to repair drift through Landing Zone Repair, Landing Zone Reset, account re-enrollment, or Control Reset via console/API.
The IaC paradox: Control Tower's console-driven nature means you can't fully version control your governance. With pure Organizations + IaC, there's no "drift" because code IS the source of truth.
AWS Config Conflicts
Config recorder conflicts: AWS Config allows only one configuration recorder per Region per account. Existing recorders must be deleted before Control Tower enrollment, causing enrollment failures if not addressed.
Why this matters: If you've previously enabled Config manually, through a third-party tool (Terraform, CloudFormation), or via organization-wide Config enablement, you'll need to remove those recorders before enrolling accounts in Control Tower.
Contrast with Organizations-only: You have full control over Config deployment. Enable it only where needed, with the configuration you choose.
SCP Limits and Policy Complexity
Attachment limits: Maximum 5 SCPs per OU or account. Control Tower consumes slots for preventive controls, leaving fewer for custom policies. This can trigger "LimitExceeded" errors.
Ownership confusion: Mix of Control Tower-managed and custom SCPs requires tracking which policies are "yours" vs managed. Modifying Control Tower SCPs directly causes drift.
Character limits: 5,120 characters per SCP. Control Tower SCPs count against this limit, constraining custom policy complexity.
Contrast with Organizations-only: Full control over all 5 SCP slots, clear ownership, IaC-managed policies without drift concerns.
For comprehensive guidance on multi-account governance best practices including OU design, policy management, and security baselines, see our detailed guide on AWS multi-account best practices.
Conclusion: Making the Right Choice
The Control Tower vs Organizations question ultimately comes down to one decision: Do you want console-driven automation or code-driven governance?
Key Takeaways
Fundamental relationship: Control Tower is built ON TOP of Organizations and REQUIRES it. They're complementary layers, not alternatives.
The clickops tradeoff: Control Tower is primarily console-driven, which conflicts with IaC/GitOps practices. For teams committed to infrastructure-as-code, this is often a dealbreaker.
-
Decision criteria:
- Organizations + IaC: For teams with DevOps maturity who want code-driven governance
- Control Tower: For teams wanting rapid console-based setup with 750+ pre-built controls
- Organizations alone: For simple use cases with minimal compliance requirements
IaC alternatives exist: CDK Landing Zone, OrgFormation, and Landing Zone Accelerator provide code-driven landing zones that work directly with Organizations.
Common challenges: Control Tower drift, Config conflicts, and SCP limits are symptoms of the clickops model.
Recommended Next Steps
If you prefer infrastructure-as-code:
- Explore AWS Control Tower alternatives for IaC-first options
- Consider CDK Landing Zone, OrgFormation, or Landing Zone Accelerator
- Work directly with AWS Organizations for full code-driven governance
If you want console-based automation:
- Control Tower provides the fastest path to a governed landing zone
- Be aware of the clickops tradeoff and ongoing drift management
- Understand you cannot make manual changes in Organizations without causing drift
For implementation guidance:
- Review our AWS SCP examples for production-ready policies
- Follow AWS Organizations best practices for governance patterns
- Reference the official AWS multi-account whitepaper for strategic design principles
AWS Organizations is the foundation for all multi-account governance. Control Tower is just one way to build on that foundation, and it's the console-driven way. For teams committed to infrastructure-as-code, alternatives that work directly with Organizations often provide better long-term maintainability and align with modern DevOps practices.
What's your experience with Control Tower vs Organizations? Have you found the clickops tradeoff acceptable, or did you go the IaC route? Share your experience in the comments below.
import { CtaCard } from "../../components/CtaCard";
Written by Danny, Founder @ towardsthecloud → Helping startups cut costs and ship faster on AWS.
FYI; I'm also building cloudburn.io → Help developers catch expensive infra in PR's before they deploy on AWS Cloud.
Top comments (0)