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I see only benefits to the onion architecture over the 3 layered architecture where the BL had responsibility to call methods on DAL (or an interface of DAL) to do CRUD. The onion has better separation of concerns, testability, maintainability and is cleaner.

So is the onion architecture indeed better in all aspects and 3 layered architecture is just an old way of doing things, or there are some scenarios where I should prefer to use the 3 layered architecture, if so - which?

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Layers, Onions, Ports, Adapters: it's all the same

Since this article makes clear that onion is equivalent to 3 layer + application of the Dependency Inversion Principle (DIP), then the question becomes "where should I prefer to use DIP?" I'd say any non-toy project. Using DIP allows the core of your code to be more isolated, testable and maintainable. When you really don't care about that is when it's a throw-away project or when you are trading maintainability for performance.

Also, don't confuse DIP with DI (Dependency Injection) containers. One doesn't imply the other.

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