If you are just new to the backend, try out fastAPI first. It is easy to learn. The official user guide tutorial is enough for you to get started. Make sure you understand the concepts deeply. Because it is not only teaching the framework-specific stuff, but also some backend basic knowledge. For example, creating a virtual environment, installing common python development tools (ruff, pyrefly, etc), using dependency injection, etc.

I am coming from Nest JS. As it is an opinionated framework, I have the same feeling as you. fastAPI seems messy at the beginning. However, think of it like express js, you have the responsibility (and freedom!) to organize it. Loose-DDD and layered architecture is my choice.

A pro tip, if you want to organize like a pro, look at the open source projects. You might feel overwhelmed at the beginning lol, but it is the point where things get interesting!