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Building a Jenkins CI/CD Pipeline on AWS EC2 for a 3-Tier Dockerized App

A hands-on walkthrough of automating deployments with Jenkins on two AWS EC2 instances, using GitHub webhooks, SSH, and Docker Compose, plus the real mistakes I hit and how I fixed them.

As a DevOps intern, I kept hearing that "CI/CD saves time," but I only understood it when I built a pipeline from scratch. In this article, I walk through how I set up Jenkins on AWS EC2 to automatically deploy a React + Node.js + MySQL application using Docker Compose, and the problems I faced along the way.
Architecture
  • Jenkins Server (EC2 #1): runs Jenkins and pulls code from GitHub
  • App Server (EC2 #2): runs the application containers
  • Flow: git push → GitHub webhook → Jenkins pipeline → SSH to App Server → docker compose up -d --build
  • I kept Jenkins and the app on separate instances so heavy builds never starve the running application.
Prerequisites
  • AWS account with two EC2 instances ([instance type], [region])
  • Security groups: SSH (22) and Jenkins (8080) from your IP, app ports open on the App Server
  • A GitHub repo containing a docker-compose.yml
  • Basic Docker knowledge
Step 1: Install Jenkins on EC2 #1
bash
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sudo apt update
sudo apt install -y fontconfig openjdk-17-jre
# add the Jenkins repo and install as per the official docs
sudo systemctl enable --now jenkins
Open http://<jenkins-public-ip>:8080, unlock with the initial admin password, and install the suggested plugins.
Step 2: Prepare the App Server (EC2 #2)
Install Docker and Docker Compose, then allow your deploy user to run Docker without sudo:
bash
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sudo usermod -aG docker $USER
Step 3: Set up SSH access from Jenkins to the App Server
Generate a key pair, add the public key to ~/.ssh/authorized_keys on the App Server, and store the private key in Jenkins credentials with an ID like app-server-ssh.
Step 4: Connect GitHub with a webhook
In the repo, go to Settings → Webhooks and add http://<jenkins-ip>:8080/github-webhook/. In the Jenkins job, enable "GitHub hook trigger for GITScm polling."
Step 5: The Jenkinsfile
groovy
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pipeline {
agent any
stages {
stage('Checkout') {
steps { git branch: 'main', url: 'https://github.com/<user>/<repo>.git' }
}
stage('Deploy to App Server') {
steps {
sshagent(['app-server-ssh']) {
sh '''
ssh -o StrictHostKeyChecking=no ubuntu@<app-server-ip> "
cd ~/app || git clone https://github.com/<user>/<repo>.git ~/app && cd ~/app
git pull origin main
docker compose down
docker compose up -d --build
"
'''
}
}
}
}
}
Step 6: Test it
Push a small change. Jenkins triggers automatically, and the updated app goes live within a couple of minutes.
Challenges I faced
  • Java version mismatch: Jenkins failed until the Java version matched its requirement.
  • Disk space: Docker images quickly fill a small root volume. Use docker system prune and size the volume properly.
  • Docker permissions: "permission denied" on the Docker socket was fixed by adding the user to the docker group and logging in again.
  • Jenkinsfile syntax errors: one missing brace cost me an hour. Use Replay and a linter.
  • Master-agent vs SSH deploy: I first tried a master-agent setup, but for simple deployments SSH from the pipeline was cleaner and easier to debug.
What I'd improve next
  • Move secrets into a proper secret store
  • Add automated test stages before deploy
  • Push images to Amazon ECR instead of building on the server
  • Add a load balancer with HTTPS
Conclusion
Building this end-to-end taught me more than any tutorial, mostly because things broke along the way. If you're learning DevOps, pick a small app, break it, and fix it. Code: https://github.com/KashfaMuskan329/3tier-jenkins-cicd-pipeline.
Questions are welcome in the comments!
Any opinions in this article are those of the individual author and may not reflect the opinions of AWS.
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