diff --git a/Makefile b/Makefile
index 776a1516d..7ee5a9809 100644
--- a/Makefile
+++ b/Makefile
@@ -16,6 +16,7 @@ build-java: ## Builds the Java code generation packages.
 
 test-protocols: ## Generates and runs the restJson1 protocol tests.
 	cd codegen && ./gradlew :protocol-test:build
+	uv pip install codegen/protocol-test/build/smithyprojections/protocol-test/rest-json-1/python-client-codegen
 	uv run pytest codegen/protocol-test/build/smithyprojections/protocol-test/rest-json-1/python-client-codegen
 
 
diff --git a/codegen/aws/core/src/main/java/software/amazon/smithy/python/aws/codegen/AwsUserAgentIntegration.java b/codegen/aws/core/src/main/java/software/amazon/smithy/python/aws/codegen/AwsUserAgentIntegration.java
index 008f3233c..423296913 100644
--- a/codegen/aws/core/src/main/java/software/amazon/smithy/python/aws/codegen/AwsUserAgentIntegration.java
+++ b/codegen/aws/core/src/main/java/software/amazon/smithy/python/aws/codegen/AwsUserAgentIntegration.java
@@ -60,7 +60,7 @@ public List<RuntimeClientPlugin> getClientPlugins(GenerationContext context) {
                                     moduleName,
                                     user_agent_plugin_file.replace('/', '.')), ".")
                             .definitionFile(String
-                                    .format("./%s/%s.py", moduleName, user_agent_plugin_file))
+                                    .format("./src/%s/%s.py", moduleName, user_agent_plugin_file))
                             .name("aws_user_agent_plugin")
                             .build())
                     .build();
@@ -90,7 +90,7 @@ public List<RuntimeClientPlugin> getClientPlugins(GenerationContext context) {
                             .addConfigProperty(uaAppId)
                             .pythonPlugin(userAgentPlugin)
                             .writeAdditionalFiles((c) -> {
-                                String filename = "%s/%s.py".formatted(moduleName, user_agent_plugin_file);
+                                String filename = "src/%s/%s.py".formatted(moduleName, user_agent_plugin_file);
                                 c.writerDelegator()
                                         .useFileWriter(
                                                 filename,
diff --git a/codegen/core/src/main/java/software/amazon/smithy/python/codegen/CodegenUtils.java b/codegen/core/src/main/java/software/amazon/smithy/python/codegen/CodegenUtils.java
index 4cba69d64..734da83a5 100644
--- a/codegen/core/src/main/java/software/amazon/smithy/python/codegen/CodegenUtils.java
+++ b/codegen/core/src/main/java/software/amazon/smithy/python/codegen/CodegenUtils.java
@@ -70,7 +70,7 @@ public static Symbol getConfigSymbol(PythonSettings settings) {
         return Symbol.builder()
                 .name("Config")
                 .namespace(String.format("%s.config", settings.moduleName()), ".")
-                .definitionFile(String.format("./%s/config.py", settings.moduleName()))
+                .definitionFile(String.format("./src/%s/config.py", settings.moduleName()))
                 .build();
     }
 
@@ -82,7 +82,7 @@ public static Symbol getPluginSymbol(PythonSettings settings) {
         return Symbol.builder()
                 .name("Plugin")
                 .namespace(String.format("%s.config", settings.moduleName()), ".")
-                .definitionFile(String.format("./%s/config.py", settings.moduleName()))
+                .definitionFile(String.format("./src/%s/config.py", settings.moduleName()))
                 .build();
     }
 
@@ -101,7 +101,7 @@ public static Symbol getServiceError(PythonSettings settings) {
         return Symbol.builder()
                 .name("ServiceError")
                 .namespace(String.format("%s.models", settings.moduleName()), ".")
-                .definitionFile(String.format("./%s/models.py", settings.moduleName()))
+                .definitionFile(String.format("./src/%s/models.py", settings.moduleName()))
                 .build();
     }
 
@@ -118,7 +118,7 @@ public static Symbol getApiError(PythonSettings settings) {
         return Symbol.builder()
                 .name("ApiError")
                 .namespace(String.format("%s.models", settings.moduleName()), ".")
-                .definitionFile(String.format("./%s/models.py", settings.moduleName()))
+                .definitionFile(String.format("./src/%s/models.py", settings.moduleName()))
                 .build();
     }
 
@@ -135,7 +135,7 @@ public static Symbol getUnknownApiError(PythonSettings settings) {
         return Symbol.builder()
                 .name("UnknownApiError")
                 .namespace(String.format("%s.models", settings.moduleName()), ".")
-                .definitionFile(String.format("./%s/models.py", settings.moduleName()))
+                .definitionFile(String.format("./src/%s/models.py", settings.moduleName()))
                 .build();
     }
 
@@ -149,7 +149,7 @@ public static Symbol getHttpAuthParamsSymbol(PythonSettings settings) {
         return Symbol.builder()
                 .name("HTTPAuthParams")
                 .namespace(String.format("%s.auth", settings.moduleName()), ".")
-                .definitionFile(String.format("./%s/auth.py", settings.moduleName()))
+                .definitionFile(String.format("./src/%s/auth.py", settings.moduleName()))
                 .build();
     }
 
@@ -163,7 +163,7 @@ public static Symbol getHttpAuthSchemeResolverSymbol(PythonSettings settings) {
         return Symbol.builder()
                 .name("HTTPAuthSchemeResolver")
                 .namespace(String.format("%s.auth", settings.moduleName()), ".")
-                .definitionFile(String.format("./%s/auth.py", settings.moduleName()))
+                .definitionFile(String.format("./src/%s/auth.py", settings.moduleName()))
                 .build();
     }
 
diff --git a/codegen/core/src/main/java/software/amazon/smithy/python/codegen/PythonSymbolProvider.java b/codegen/core/src/main/java/software/amazon/smithy/python/codegen/PythonSymbolProvider.java
index 19a4e2f96..4c7907983 100644
--- a/codegen/core/src/main/java/software/amazon/smithy/python/codegen/PythonSymbolProvider.java
+++ b/codegen/core/src/main/java/software/amazon/smithy/python/codegen/PythonSymbolProvider.java
@@ -408,7 +408,7 @@ private SymbolReference createSchemaSymbol(Shape shape) {
         } else {
             schemaSymbolBuilder
                     .namespace(String.format("%s.%s", settings.moduleName(), SCHEMAS_FILE.replace('/', '.')), ".")
-                    .definitionFile(String.format("./%s/%s.py", settings.moduleName(), SCHEMAS_FILE));
+                    .definitionFile(String.format("./src/%s/%s.py", settings.moduleName(), SCHEMAS_FILE));
         }
         var schemaSymbol = schemaSymbolBuilder.build();
         return SymbolReference.builder()
@@ -428,7 +428,7 @@ private Symbol.Builder createGeneratedSymbolBuilder(
             boolean includeSchema
     ) {
         var namespace = String.format("%s.%s", settings.moduleName(), file.replace('/', '.'));
-        var filename = String.format("./%s/%s.py", settings.moduleName(), file);
+        var filename = String.format("./src/%s/%s.py", settings.moduleName(), file);
         return createSymbolBuilder(shape, typeName, includeSchema)
                 .namespace(namespace, ".")
                 .definitionFile(filename);
diff --git a/codegen/core/src/main/java/software/amazon/smithy/python/codegen/generators/InitGenerator.java b/codegen/core/src/main/java/software/amazon/smithy/python/codegen/generators/InitGenerator.java
index ca0432f4d..22b7e156d 100644
--- a/codegen/core/src/main/java/software/amazon/smithy/python/codegen/generators/InitGenerator.java
+++ b/codegen/core/src/main/java/software/amazon/smithy/python/codegen/generators/InitGenerator.java
@@ -42,7 +42,7 @@ public void run() {
         }
         context.writerDelegator()
                 .useFileWriter(
-                        "%s/__init__.py".formatted(context.settings().moduleName()),
+                        "src/%s/__init__.py".formatted(context.settings().moduleName()),
                         w -> w.write("__version__: str = $S", context.settings().moduleVersion()));
     }
 }
diff --git a/codegen/core/src/main/java/software/amazon/smithy/python/codegen/generators/ProtocolGenerator.java b/codegen/core/src/main/java/software/amazon/smithy/python/codegen/generators/ProtocolGenerator.java
index 48fe8b663..deca9d40d 100644
--- a/codegen/core/src/main/java/software/amazon/smithy/python/codegen/generators/ProtocolGenerator.java
+++ b/codegen/core/src/main/java/software/amazon/smithy/python/codegen/generators/ProtocolGenerator.java
@@ -69,7 +69,7 @@ default Symbol getSerializationFunction(GenerationContext context, ToShapeId sha
         return Symbol.builder()
                 .name(getSerializationFunctionName(context, shapeId))
                 .namespace(format("%s.serialize", context.settings().moduleName()), "")
-                .definitionFile(format("./%s/serialize.py", context.settings().moduleName()))
+                .definitionFile(format("./src/%s/serialize.py", context.settings().moduleName()))
                 .build();
     }
 
@@ -96,7 +96,7 @@ default Symbol getDeserializationFunction(GenerationContext context, ToShapeId s
         return Symbol.builder()
                 .name(getDeserializationFunctionName(context, shapeId))
                 .namespace(format("%s.deserialize", context.settings().moduleName()), "")
-                .definitionFile(format("./%s/deserialize.py", context.settings().moduleName()))
+                .definitionFile(format("./src/%s/deserialize.py", context.settings().moduleName()))
                 .build();
     }
 
@@ -113,7 +113,7 @@ default Symbol getErrorDeserializationFunction(GenerationContext context, ToShap
         return Symbol.builder()
                 .name("_deserialize_error_" + CaseUtils.toSnakeCase(name))
                 .namespace(format("%s.deserialize", context.settings().moduleName()), "")
-                .definitionFile(format("./%s/deserialize.py", context.settings().moduleName()))
+                .definitionFile(format("./src/%s/deserialize.py", context.settings().moduleName()))
                 .build();
     }
 
diff --git a/codegen/core/src/main/java/software/amazon/smithy/python/codegen/generators/SchemaGenerator.java b/codegen/core/src/main/java/software/amazon/smithy/python/codegen/generators/SchemaGenerator.java
index 7711d97ba..daaccadaa 100644
--- a/codegen/core/src/main/java/software/amazon/smithy/python/codegen/generators/SchemaGenerator.java
+++ b/codegen/core/src/main/java/software/amazon/smithy/python/codegen/generators/SchemaGenerator.java
@@ -207,7 +207,7 @@ private void writeSchemaMembers(PythonWriter writer, Shape shape) {
     // references, but when generating schemas we need to instead defer creating those
     // members until all schemas exist.
     public void finalizeRecursiveShapes() {
-        var filename = String.format("%s/_private/schemas.py", context.settings().moduleName());
+        var filename = String.format("src/%s/_private/schemas.py", context.settings().moduleName());
         var namespace = String.format("%s._private.schemas", context.settings().moduleName());
         context.writerDelegator().useFileWriter(filename, namespace, this::finalizeRecursiveShapes);
     }