diff --git a/gazelle/python/generate.go b/gazelle/python/generate.go
index 27930c1025..49a599120b 100644
--- a/gazelle/python/generate.go
+++ b/gazelle/python/generate.go
@@ -85,8 +85,6 @@ func (py *Python) GenerateRules(args language.GenerateArgs) language.GenerateRes
 			if parent != nil && parent.CoarseGrainedGeneration() {
 				return language.GenerateResult{}
 			}
-		} else if !hasEntrypointFile(args.Dir) {
-			return language.GenerateResult{}
 		}
 	}
 
diff --git a/gazelle/python/testdata/relative_imports/BUILD.in b/gazelle/python/testdata/relative_imports/BUILD.in
index c04b5e5434..1059942bfb 100644
--- a/gazelle/python/testdata/relative_imports/BUILD.in
+++ b/gazelle/python/testdata/relative_imports/BUILD.in
@@ -1 +1,2 @@
 # gazelle:resolve py resolved_package //package2:resolved_package
+# gazelle:python_generation_mode project
diff --git a/gazelle/python/testdata/relative_imports/BUILD.out b/gazelle/python/testdata/relative_imports/BUILD.out
index bf9524480a..fa25c133c6 100644
--- a/gazelle/python/testdata/relative_imports/BUILD.out
+++ b/gazelle/python/testdata/relative_imports/BUILD.out
@@ -1,6 +1,7 @@
 load("@rules_python//python:defs.bzl", "py_binary", "py_library")
 
 # gazelle:resolve py resolved_package //package2:resolved_package
+# gazelle:python_generation_mode project
 
 py_library(
     name = "relative_imports",
diff --git a/gazelle/python/testdata/subdir_sources/BUILD.in b/gazelle/python/testdata/subdir_sources/BUILD.in
index e69de29bb2..adfdefdc8a 100644
--- a/gazelle/python/testdata/subdir_sources/BUILD.in
+++ b/gazelle/python/testdata/subdir_sources/BUILD.in
@@ -0,0 +1 @@
+# gazelle:python_generation_mode project
diff --git a/gazelle/python/testdata/subdir_sources/BUILD.out b/gazelle/python/testdata/subdir_sources/BUILD.out
index d03a8f05ac..5d77890d4f 100644
--- a/gazelle/python/testdata/subdir_sources/BUILD.out
+++ b/gazelle/python/testdata/subdir_sources/BUILD.out
@@ -1,5 +1,8 @@
+
 load("@rules_python//python:defs.bzl", "py_binary")
 
+# gazelle:python_generation_mode project
+
 py_binary(
     name = "subdir_sources_bin",
     srcs = ["__main__.py"],