A Pragmatic Guide to Spring Boot Architecture: Choosing Between Three-Layer and Clean Architecture

Software architecture is the foundational blueprint that determines the long-term success of an application. For developers working with Spring Boot, architectural choices have a direct impact on maintainability, scalability, and overall development productivity. A poorly chosen structure can result in a codebase that is hard to test, expensive to modify, and slow to evolve. Among the available patterns, Three-Layer Architecture and Clean Architecture are two of the most frequently used approaches. The former emphasizes simplicity and delivery speed, while the latter focuses on domain-centric design and long-term flexibility. This guide provides a clear, comparative analysis of both architectures, complete with practical examples, to help teams make informed decisions based on their project’s goals and constraints.

1. Three-Layer Architecture: Designed for Simplicity and Speed

1.1. Core Concepts and Structure

Three-Layer Architecture is a traditional, widely adopted pattern that separates an application into logical layers with clear responsibilities. Its straightforward design makes it appealing for projects where rapid delivery is the primary objective.

The architecture consists of three layers:

• Presentation Layer (API/UI): Handles incoming requests, validates input, and maps data to the appropriate service operations.
• Business Logic Layer (Service): Contains all the business rules and processing logic. It coordinates data processing and delegates persistence tasks to the repository layer.
• Data Access Layer (Repository): Responsible solely for data persistence—retrieving, saving, and updating data in storage systems.

The key characteristic of this architecture is its top-down dependency flow: Presentation → Service → Repository.

Because of this structure, the business layer is tightly coupled to specific data-access technologies—a limitation that Clean Architecture directly addresses.

1.2. Practical Spring Boot Example

Below is a simple example showing how a product creation flow might be implemented using Three-Layer Architecture.

(a) Presentation Layer (Controller)

// ProductController.java
@RestController
@RequestMapping("/products")
public class ProductController {

    @Autowired
    private ProductService productService;

    @PostMapping
    public ResponseEntity<String> createProduct(@RequestBody ProductRequest productRequest) {
        if (productRequest.getName() == null || productRequest.getPrice() <= 0) {
            return ResponseEntity.badRequest().body("Invalid product details.");
        }
        productService.submitNewProduct(productRequest);
        return ResponseEntity.ok("Product successfully created.");
    }
}

(b) Business Logic Layer (Service)

// ProductService.java
@Service
public class ProductService {

    @Autowired
    private ProductRepository productRepository;

    public void submitNewProduct(ProductRequest request) {
        double finalPrice = request.getPrice() * 1.10;
        ProductEntity newProduct = new ProductEntity(request.getName(), finalPrice);
        productRepository.save(newProduct);
    }
}

(c) Data Access Layer (Repository)

// ProductRepository.java
@Repository
public interface ProductRepository extends JpaRepository<ProductEntity, Long> {
    boolean existsByName(String name);
}

1.3. Pros and Cons

While excellent for quickly getting a project off the ground, this architecture can become difficult to maintain as business complexity increases.

2. Clean Architecture: Designed for Domain Centricity and Testability

2.1. Core Principles and the Dependency Rule

Clean Architecture is built on the idea that the most critical business logic should be completely independent of external technologies. Inspired by SOLID principles and the Dependency Inversion Principle, it organizes the system into concentric layers where dependencies always point inward.

The Dependency Rule: Inner layers must not depend on outer layers.

Key layers include:

• Entities (Domain Layer): Core business rules and domain objects.
• Use Cases (Application Layer): Application-specific rules that orchestrate interactions between domain objects.
• Interface Adapters: Translate data between internal and external formats.
• Frameworks & Drivers: The outermost layer containing controllers, repositories, and framework-specific code.

This structure ensures that domain and use case logic remain stable even when frameworks or infrastructure change.

2.2. Practical Spring Boot Example

A user registration flow demonstrates how Clean Architecture structures responsibilities.

• Entities: Contain core business rules such as password validation.
• Use Case (Interactor): Orchestrates the registration process.
• Input/Output Boundaries: Define ports for communication between layers.
• Controllers and Adapters: Convert external input (HTTP requests) into internal formats and invoke use cases.
• Repository Adapters: Implement the repository interface using technologies like JPA.

2.3. Pros and Cons

3. Feature Comparison

4. Decision Framework: Choosing the Right Architecture

4.1. When to Choose Each Architecture

4.2. Practical Questions for Technical Leads

• What is the expected lifespan of the project?
• How complex are the business rules?
• What is the team’s experience with advanced design principles?
• Do we anticipate major changes to infrastructure or UI channels?

4.3. Migration Strategy: From Three-Layer to Clean Architecture

A gradual migration is a practical approach:

1. Identify core business logic hidden inside service classes.
2. Extract this logic into explicit Use Case classes.
3. Define repository interfaces in the application layer.
4. Create adapters implementing those interfaces (e.g., JPA).
5. Migrate one module at a time, supported by comprehensive tests.
6. Refactor controllers to interact with use cases instead of services.

5. When Both Use Controller / Service / Repository: What Is the Real Difference?

Although the names of the layers may be the same, their responsibilities differ significantly between the two architectures.

5.1. Controller Differences

Key insight: In Three-Layer, controllers may contain business logic. In Clean Architecture, controllers are strictly translators.

5.2. Service Differences (The Most Important Distinction)

Three-Layer Service example:

OrderService.createOrder()
  - Validate product
  - Validate inventory
  - Apply promotion rules
  - Create order
  - Save to DB

Clean Architecture Use Case:

CreateOrderUseCase.execute()
  - Validate flow
  - Use domain rules
  - Persist through repository port

Key insight: Three-Layer Service = “business logic container” Clean Service = “use case orchestrator”

5.3. Repository Differences

Three-Layer:

Service → UserRepository (JPA)

Clean Architecture:

UseCase → UserRepositoryPort ← JpaUserRepositoryAdapter

Key insight: Use cases never depend on JPA or database details.