Maintaining the security and compliance of your cloud infrastructure is non-negotiable. Managing patches and maintaining system compliance at scale is a significant part of that. However, manual patching processes are often time-consuming and prone to errors, which can lead to security vulnerabilities and compliance gaps.

Amazon provides AWS Systems Manager as part of its managed cloud services to streamline this task. AWS Systems Manager provides built-in capabilities to simplify and automate patching workflows, ensuring systems remain compliant with organizational and regulatory standards.

This article delves into the workings of AWS Systems Manager’s Patch Manager and Compliance Manager, exploring how they collaborate to automate patching, enforce baselines, and provide centralized compliance visibility. We will also cover best practices and integration patterns that enable scalable, secure patch governance.

Overview of AWS Systems Manager

AWS Systems Manager (SSM) is a collection of tools that allow systems administrators and DevSecOps teams to manage Amazon EC2 instances, on-premises infrastructure, and hybrid environments.

SSM is a powerful and versatile cloud platform that provides a unified interface for viewing operational data and automating operational tasks across your AWS resources.

AWS Systems Manager is composed of several services, each designed to address specific operational needs:

1. Patch Manager

Patch Manager automates patching for operating systems and applications. It simplifies the complex task of keeping your operating systems and applications up to date, which is critical for mitigating vulnerabilities and maintaining compliance.

2. Compliance Manager

The Compliance Manager provides visibility to see whether your instances are compliant with patching, configuration, and policy requirements. It tracks compliance status of cases based on patch and configuration state.

3. State Manager

This service helps you define and maintain the desired state of your instances. For example, if you want all your servers to use specific security settings, State Manager automatically applies the settings or rules you define.  

4. Command Line Interface (CLI)

CLI helps you execute repeatable operational tasks securely. One of the primary strengths of Systems Manager is its ability to automate common and repetitive IT operations and management tasks. This is achieved through the use of Command Line Interface. CLI executes JSON/YAML documents that define specific tasks or workflows.

5. Session Manager and Run Command

Run Command enables you to execute commands and scripts on your managed instances at scale. At the same time, Session Manager provides secure and auditable access to your managed cases without requiring the opening of inbound ports. Together, these components offer a unified solution for patch orchestration and compliance reporting.

Patch management with Patch Manager

The patch manager is a critical component for maintaining the security and operational health of your managed instances. It automates the often-complex and time-consuming process of applying security updates and other types of patches across your Amazon EC instances, on-premises servers, and virtual machines (VMs).

Here are some of the key elements in Patch Manager you should know about before you start using it for patch management:

Prerequisites

•  These are the prerequisites before you can use Patch Manager to scan or install updates on your EC2 instances. EC2 instances must have the SSM Agent installed and running. Without the agent, AWS Systems Manager can’t send commands or perform patching.

• Your EC2 instances require IAM roles to communicate securely with AWS services. Instances should be assigned an IAM role with the AmazonSSMManagedInstanceCore policy.
• Your instances require a method to communicate with AWS Systems Manager to receive patch instructions and send back results. Network access to Systems Manager can be configured through either the public internet or VPC Endpoints in the case of a private subnet.

Patch Baselines

In short, Patch Baselines define the rules for approving or rejecting patches. These rules enable you to approve or deny patches based on your specific criteria automatically.

There are types of Patch Baselines you can use:

· Default baselines

AWS provides predefined baselines for various operating systems, such as Ubuntu, Windows Server, and Amazon Linux. These baselines include a standard set of rules that are updated and maintained by AWS.

· Custom baselines

Custom baselines are user-defined patch policies that give you complete control over which patches to approve or reject.  You can define specific approval rules and compliance thresholds to suit your needs. Custom baselines are ideal for those working in regulated industries with strict compliance standards.

 You can set up a custom baseline to define what OS type and version to update. It also allows for auto-approval delays, which means you can automatically approve a patch after a certain number of days following its release.

Moreover, you can also define patch severity levels, such as critical, security updates only, or low importance. This helps in prioritizing the application of high-impact security fixes.

Patch Groups

Patch Groups are a way to organize your EC2 instances into different groups, each following its own baselines. They are logical collections of instances, defined using EC2 tags, i.e., PatchGroup = ProductionLinux. For that purpose, baselines are associated with Patch Groups for targeted patching control.

Scheduling patching with State Manager

Patch Manager can be integrated with State Manager to automate patch execution. Follow these steps to schedule patching with State Manager:

1. Navigate to Systems Manager > State Manager > Create Association.
2. Select the document: AWS-RunPatchBaseline.
3. Define instance targets using EC2 tags or resource groups.
4. Set a schedule using cron expressions (e.g., every Sunday at 2 AM).
5. Enable logging to Amazon S3 or CloudWatch Logs for traceability.

This creates a scheduled task that runs the patch process automatically, eliminating the need for manual intervention.

Compliance tracking and visibility

After patching, AWS Systems Manager automatically records compliance status under the Compliance section. This means that with every run, your environment is scanned and evaluated.

Each run of AWS-RunPatchBaseline generates compliance items that are classified as:

• Compliant: All required patches are successfully applied.
• Non-compliant: Some critical updates are missing.
• Unknown: The system was unable to determine the status due to connectivity issues or missing permissions.

Moreover, AWS presents this data in a real-time dashboard. IT teams can filter Compliance reports by:

• Patch group
• Instance ID
• Severity
• Compliance type

This dashboard provides real-time visibility into patch status across environments. The data is accessible via the AWS Console, AWS CLI, and API for integration with SIEM or compliance tools.

Remediation Automation

Detecting a compliance issue is just the first step. Next, you need to fix it, and doing it automatically is the preferred way. AWS has integrated Patch Manager with EventBridge, which is a rules engine that listens for specific events.

Here is how non-compliant instances can be automatically remediated by integrating with it:

• AWS EventBridge: Detects non-compliance events.
• SSM Automation Documents (SSM Docs): Define remediation workflows.
• Lambda Functions: Trigger custom logic.

Here is an example flow to help you understand better:

1. Compliance Manager flags an instance as non-compliant.
2. EventBridge rule triggers an SSM Automation runbook.
3. The runbook executes AWS-RunPatchBaseline on the instance.
4. Logs are updated and compliance state is re-evaluated.

This pattern enables self-healing infrastructure with minimal human involvement.

Integration with AWS Config and Security Hub

AWS Systems Manager can seamlessly integrate with other key AWS services to amplify its capabilities. To enforce compliance across accounts, follow these steps:

• Use AWS Config to record patch compliance state changes.
• Enable AWS Config Aggregators to unify reporting across organizations.
• Integrate with AWS Security Hub for centralized visibility and alert correlation.

Custom AWS Config rules can be written to trigger alerts or remediation based on patch compliance status.

The Cloud security hub can consume compliance findings and notify relevant teams or tools for action. Together, these integrations provide a holistic view of your infrastructure’s compliance and security posture.

Best practices

Here are some of the best practices to implement patch management in AWS Systems Manager:

Recommendation	Description
Use Tags for Patch Groups	Organize instances logically to apply patch baselines with minimal configuration.
Enable Detailed Logging	Store logs in S3 or CloudWatch for auditing, troubleshooting, and compliance reviews.
Automate with State Manager	Run scheduled patch jobs using cron-based automation.
Monitor with Compliance Manager	Track real-time patch status and alert on non-compliance.
Integrate with Security Services	Connect with AWS Config, Security Hub, and EventBridge for automated governance.

Use Case: Enterprise-level patch governance

An enterprise-level use case would be the best way to understand patch governance practically. Large enterprises manage software patches across a vast IT infrastructure; therefore, this complexity helps you understand the technical execution and strategic oversight of the entire process.

Scenario: An enterprise with 500 EC2 instances across development, staging, and production environments needs to ensure monthly patch compliance for security audits.

Solution:

• Define custom patch baselines per environment.
• Assign EC2 tags for PatchGroup values (e.g., PatchGroup=ProdLinux).
• Automate patching using State Manager with time-based scheduling.
• Store logs in CloudWatch and enable compliance notifications via EventBridge.
• Connect Systems Manager compliance data to AWS Security Hub and AWS Config.

Results:

• 90% reduction in manual patching time.
• Continuous compliance visibility.
• Audit readiness with centralized evidence.

Conclusion

Predictability is almost like a superpower in modern cloud computing. And AWS Systems Manager provides predictability through a robust framework for patch automation and compliance enforcement.

Using Patch Manager and Compliance Manager, businesses can automate routine patching and compliance tasks, which makes security a continuous part of their daily operations.

Implementing these tools in conjunction with best practices enables teams to transition from reactive patch management to proactive compliance assurance, aligning their infrastructure operations with security and governance requirements at scale.

Partner with Xavor to secure your cloud infrastructure on AWS and Azure. Our certified cloud experts can help you implement AWS Systems Manager to make the most meaningful shift in your enterprise computing.

Contact us now at [email protected] to talk to our experts.