To deploy an image generation pipeline built with Comf UI behind an API endpoint, it's necessary to first build and export the project in a specific format using Truss. This involves setting up a Baseten account and API key, installing Truss, cloning the prepared project, deploying the model to Baseten, and linking the workflow JSON file and model weights. Once deployed, users can call the model endpoint with parameters such as positive prompt, negative prompt, controlnet image, and seed, and retrieve the generated images in base64 format. The process allows developers to share and use Comf UI pipelines in applications.