Is there a way to activate a conda environment inside of a Docker image before Prefect tries to pip install prefect? And also before it tries to run the flow in that container?

If you're using the Docker Storage during a

.register(build=True)

, all of that is handled for you. The way I've handled situations like that before, is to use a

base_image

where that image is already activated to the specified environment, so when Prefect adds the Flow to it, it's exactly as you want it.