Running multiple applications on a single server using Docker is common practice, especially for small to medium businesses or developers managing several projects. But as the number of containers grows, so does the complexity. Without proper organization, you end up with a chaotic list of containers that's difficult to manage, monitor, and troubleshoot.

In this guide, I'll share practical patterns for structuring your Docker environment to keep things clean, scalable, and maintainable.

The Problem with a Flat Container Structure

When you run everything from a single docker-compose.yml file or deploy containers without a clear naming strategy, you quickly lose track of what belongs where. Imagine having two Magento stores, three React applications, shared databases, Redis instances, and various microservices — all showing up as a single flat list when you run docker ps. Finding the right container becomes a guessing game.

Separate Docker Compose Projects

The first and most impactful change you can make is organizing your applications into separate Docker Compose projects. Each application gets its own directory with its own docker-compose.yml file.

A typical structure might look like this: your main apps directory contains subdirectories for each application — perhaps two Magento stores, a React site, and a shared-services folder for infrastructure components like your reverse proxy and databases.

Docker Compose automatically prefixes container names with the project directory name, but you can also set this explicitly using the name property in your compose file. This transforms generic container names like "php-1" and "nginx-1" into descriptive names like "shop1-php-1" and "shop1-nginx-1".

Network Isolation

Docker networks provide logical separation between your applications. Each project should have its own internal network for communication between its services, while sharing a common proxy network for external access.

Your shared services define the proxy network, and individual applications join both their own internal network and the shared proxy network. This approach ensures that containers from different projects can't accidentally communicate with each other while still allowing the reverse proxy to route traffic to all applications.

Labels for Filtering and Organization

Docker labels are metadata attached to containers that enable powerful filtering capabilities. By adding labels for project name, client, or application type, you can quickly filter your container list.

For example, labeling containers with their client name and application type lets you run commands like docker ps --filter "label=client=acme" to see only containers for a specific client, or filter by application type to see all your Magento installations at once.

Creating shell aliases that leverage these filters can significantly speed up your daily workflow. A simple alias that formats docker ps output and pipes it through grep makes finding specific containers trivial.

The Reverse Proxy Pattern

One of the most common questions when running multiple web applications is how to handle ports. If all your Magento stores need port 80, how do you avoid conflicts?

The answer is simple: don't expose application ports to the host at all. Instead, use a reverse proxy that's the only service bound to ports 80 and 443. All other containers communicate through internal Docker networks, and the reverse proxy routes incoming requests based on the hostname.

This pattern has several advantages. You don't need to remember arbitrary port numbers. SSL termination happens in one place. Adding new applications doesn't require port planning. And your actual application containers remain unexposed to the outside world.

Two popular options exist for implementing this pattern. The nginx-proxy container is the simpler choice — it watches the Docker socket and automatically configures routing based on environment variables you set on your containers. Just add a VIRTUAL_HOST variable to any container, and nginx-proxy handles the rest.

Traefik offers more features at the cost of slightly more configuration. It includes a built-in dashboard for visualizing your routing, native Let's Encrypt integration for automatic SSL certificates, and powerful middleware capabilities for authentication, rate limiting, and more. For environments with many applications, the dashboard alone makes Traefik worth considering.

Visual Management with Portainer

For those who prefer a graphical interface, Portainer provides a web-based UI for managing Docker environments. Its Stacks view groups containers by their compose project, making it easy to see which containers belong together. It's particularly useful for teams where not everyone is comfortable with command-line tools.

Bringing It All Together

A well-organized Docker environment on a single server follows these principles: each application lives in its own compose project with descriptive naming, networks provide isolation between projects while enabling shared infrastructure access, a reverse proxy handles all incoming traffic and routes based on hostname, and labels enable quick filtering when you need to find specific containers.

This structure scales well from a handful of containers to dozens of applications. More importantly, it makes your infrastructure understandable — both for you six months from now and for anyone else who needs to work with it.

Start by reorganizing one application at a time. Set up your reverse proxy first, migrate your applications to separate compose projects, and gradually add labels and tooling as needed. The investment in organization pays dividends every time you need to debug an issue or deploy a new application.