Automate EC2 Maintenance with AWS Systems Manager

As enterprises scale their cloud infrastructure, managing thousands of EC2 instances becomes increasingly complex. Manual intervention for basic system maintenance — such as patching, disk cleanup, and compliance scanning — doesn’t just consume valuable engineering hours; it also introduces risk through inconsistent execution and delayed responses to vulnerabilities.

This is where AWS Systems Manager (SSM) becomes a crucial operational pillar. It provides a unified, scalable, and agent-based solution for automating maintenance workflows, enforcing compliance, and standardizing configuration management across massive EC2 fleets.

In this post, we’ll explore how to use AWS Systems Manager to automate patch management, disk cleanup, and compliance scanning with zero-touch efficiency. We’ll also dive into real-world use cases involving SSM Automation Documents and Run Command, equipping your teams with the practical knowledge to streamline EC2 operations at scale.

The Challenge of EC2 Fleet Maintenance at Scale

In traditional environments, sysadmins might SSH into servers to run updates or clean disk space. But in cloud-native operations, that model simply doesn’t scale. Consider the following pain points:

To eliminate these inefficiencies, organizations are adopting automation-first strategies using AWS Systems Manager.

What Is AWS Systems Manager?

AWS Systems Manager (SSM) is a hybrid operations tool that provides visibility and control of infrastructure on AWS and on-premises. Key features include:

Let’s explore how to automate three essential tasks using SSM.

1. Automated Patch Management

Problem:

Keeping your OS and applications up to date across hundreds or thousands of EC2 instances is critical — and error-prone when done manually.

Solution:

Use AWS Systems Manager Patch Manager to automate the process. Patch Manager allows you to define patch baselines, schedule patching windows, and enforce maintenance compliance across all managed nodes.

Implementation Highlights:

Example Run Command:

aws ssm send-command \
  --document-name "AWS-RunPatchBaseline" \
  --targets "Key=tag:Environment,Values=Production" \
  --parameters 'Operation=Install' \
  --comment "Install latest approved patches" \
  --region us-west-2

Automation:

Use a combination of State Manager associations and Maintenance Windows to trigger patching automatically on a schedule (e.g., Sundays at 2 AM).

2. Disk Cleanup Automation

Problem:

Over time, EC2 instances accumulate orphaned temp files, logs, and package caches — leading to wasted storage and performance degradation.

Solution:

Use Run Command or SSM Automation Documents to schedule periodic cleanup tasks.

Custom SSM Document: DiskCleanupDocument

Create a custom SSM Automation Document to:

Sample Bash Script:

#!/bin/bash
rm -rf /tmp/*
rm -rf /var/tmp/*
find /var/log -type f -name "*.log" -mtime +7 -exec truncate -s 0 {} \;
yum clean all

Execute via Run Command:

aws ssm send-command \
  --document-name "AWS-RunShellScript" \
  --targets "Key=tag:Role,Values=AppServer" \
  --parameters 'commands=["/path/to/cleanup-script.sh"]' \
  --comment "Disk cleanup operation" \
  --region us-west-2

Or package this into a custom SSM Automation Document that includes pre-checks (e.g., disk space threshold) and post-actions (e.g., logging to CloudWatch Logs).

3. Compliance Scanning

Problem:

Auditing systems for compliance — patch status, configuration state, installed software — is time-consuming without a centralized mechanism.

Solution:

SSM provides Inventory, Patch Compliance, and Automation to gather compliance data and take corrective actions automatically.

How to Use:

Example: Auto-Remediate Non-Compliant Patches

SSM Document Example: AutoRemediatePatches

{
  "description": "Automatically reapply patches on non-compliant instances",
  "mainSteps": [
    {
      "action": "aws:runCommand",
      "name": "RePatch",
      "inputs": {
        "DocumentName": "AWS-RunPatchBaseline",
        "Parameters": {
          "Operation": ["Install"]
        }
      }
    }
  ]
}

Schedule or trigger this via CloudWatch Events for dynamic compliance remediation.

Real-World Use Cases for SSM Automation and Run Command

1. Golden Image Validation

Use an SSM Automation Document to validate AMI configurations (patch level, agent versions, etc.) before promoting them to production.

2. On-Demand Troubleshooting

Launch a Run Command to collect logs or execute diagnostics on impacted EC2 instances — without SSH access or bastion hosts.

3. Application Restart

Gracefully restart services (e.g., NGINX, Apache, Java apps) across a fleet using Run Command tied to EC2 tags or instance IDs.

4. Security Incident Response

Automatically isolate EC2 instances by modifying security group rules or stopping services using a triggered SSM Automation runbook.

Best Practices

Conclusion

Scaling cloud operations requires more than provisioning tools — it demands intelligent automation. AWS Systems Manager provides a powerful, agent-driven framework for automating critical EC2 maintenance tasks like patching, disk cleanup, and compliance enforcement at scale.

By leveraging SSM Automation Documents and Run Command, IT operations teams can eliminate toil, enhance security posture, and maintain operational consistency across sprawling cloud environments — without ever logging into a single instance.

As your infrastructure grows, let automation handle the routine, so your engineers can focus on innovation.

Need help implementing this across your organization?

Contact our experts today to design, deploy, and manage automated EC2 maintenance solutions tailored to your cloud environment.