AWS Systems Manager: Secure Operations and Patch Management

Part of the Cybersecurity Skills Guide — This article is one deep-dive in our complete guide series.

By HADESS Team | February 28, 2026 | Updated: February 28, 2026 | 5 min read

Systems Manager (SSM) is often categorized as an operations tool, but its security impact is significant. Session Manager replaces SSH bastion hosts. Patch Manager automates vulnerability remediation. Parameter Store holds secrets. State Manager enforces configuration compliance. If you are running EC2 instances without SSM, you are making security harder than it needs to be.

Session Manager

Session Manager provides shell access to EC2 instances without opening inbound ports, managing SSH keys, or maintaining bastion hosts. It works through the SSM agent, which makes outbound HTTPS connections to the SSM service endpoint.

Security advantages over SSH:

• No port 22 open in security groups
• No SSH key distribution or rotation
• IAM-based access control — who can start sessions to which instances
• Full session logging to S3 and CloudWatch — every command typed, every output returned
• Integration with CloudTrail for session start/stop auditing

Enable KMS encryption for session data in transit. Configure S3 logging with a dedicated bucket and object lock retention. Set up CloudWatch Logs streaming for real-time monitoring of session activity.

Restrict Session Manager access with IAM policies using the ssm:StartSession action with conditions on ssm:resourceTag to control which instances specific roles can access.

Patch Manager

Patch Manager defines patch baselines, scans for missing patches, and applies them on a schedule. Configure it properly and you have automated, auditable vulnerability remediation.

Create custom patch baselines per operating system. Define which patches are auto-approved: critical and security patches should auto-approve after a short testing window (3-7 days). Define maintenance windows for patching so instances are not rebooted during business hours.

Use Patch Manager compliance data to track patch coverage across your fleet. Instances that fall out of compliance should trigger notifications. Feed compliance data into Security Hub for centralized tracking.

For immutable infrastructure, Patch Manager still has value: use it for scanning only (without applying patches) to validate that your AMI pipeline is producing fully patched images.

Parameter Store

Parameter Store holds configuration values and secrets. Use SecureString parameters with a customer-managed KMS key for anything sensitive: database passwords, API keys, license keys.

Parameter Store supports parameter policies for expiration and notification. Set an expiration policy on credentials so you get an EventBridge notification before they expire, forcing rotation.

For secrets that require automatic rotation (database credentials, OAuth tokens), use Secrets Manager instead. Parameter Store does not have built-in rotation. Use Parameter Store for configuration values that change infrequently and Secrets Manager for credentials that need rotation.

Organize parameters with a hierarchy: /prod/app-name/db-password, /staging/app-name/api-key. Use IAM policies to grant access at the path level so teams can only read their own parameters.

State Manager

State Manager applies configurations to your fleet on a schedule. Use it to enforce security baselines:

• Install and configure the CloudWatch agent
• Apply CIS benchmark settings
• Ensure the SSM agent stays current
• Verify that required security agents are running

State Manager associations run on a schedule you define. If an instance drifts from the desired state, the next association run corrects it automatically.

Next Steps

• Assess your operations security knowledge with the assessment tool
• Review automation and operations topics in the skills library
• Build a study plan with the coaching tool covering SSM and infrastructure security

Related Guides in This Series

• Active Directory Security: Attack Paths and Hardening — HADESS | 2026
• AWS ALB Security: TLS, Authentication, and Access Controls — HADESS | 2026
• AWS CloudTrail: Log Analysis and Security Monitoring — HADESS | 2026

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