diff --git a/gazelle/python/generate.go b/gazelle/python/generate.go
index 5ab9f53c79..1eed5f53ce 100644
--- a/gazelle/python/generate.go
+++ b/gazelle/python/generate.go
@@ -238,9 +238,13 @@ func (py *Python) GenerateRules(args language.GenerateArgs) language.GenerateRes
 		}
 
 		if !hasPyBinaryEntryPointFile {
-			sort.Strings(mainModules)
 			// Creating one py_binary target per main module when __main__.py doesn't exist.
-			for _, filename := range mainModules {
+			mainFileNames := make([]string, 0, len(mainModules))
+			for name := range mainModules {
+				mainFileNames = append(mainFileNames, name)
+			}
+			sort.Strings(mainFileNames)
+			for _, filename := range mainFileNames {
 				pyBinaryTargetName := strings.TrimSuffix(filepath.Base(filename), ".py")
 				if err := ensureNoCollision(args.File, pyBinaryTargetName, actualPyBinaryKind); err != nil {
 					fqTarget := label.New("", args.Rel, pyBinaryTargetName)
@@ -248,13 +252,10 @@ func (py *Python) GenerateRules(args language.GenerateArgs) language.GenerateRes
 						fqTarget.String(), actualPyBinaryKind, err)
 					continue
 				}
-				binaryDeps := allDeps.Select(func(index int, value interface{}) bool {
-					return value.(module).Filepath == filepath.Join(args.Rel, filename)
-				})
 				pyBinary := newTargetBuilder(pyBinaryKind, pyBinaryTargetName, pythonProjectRoot, args.Rel, pyFileNames).
 					addVisibility(visibility).
 					addSrc(filename).
-					addModuleDependencies(binaryDeps).
+					addModuleDependencies(mainModules[filename]).
 					generateImportsAttribute().build()
 				result.Gen = append(result.Gen, pyBinary)
 				result.Imports = append(result.Imports, pyBinary.PrivateAttr(config.GazelleImportsKey))
diff --git a/gazelle/python/parser.go b/gazelle/python/parser.go
index d22850b6a9..9b00b831e9 100644
--- a/gazelle/python/parser.go
+++ b/gazelle/python/parser.go
@@ -101,7 +101,7 @@ func newPython3Parser(
 
 // parseSingle parses a single Python file and returns the extracted modules
 // from the import statements as well as the parsed comments.
-func (p *python3Parser) parseSingle(pyFilename string) (*treeset.Set, []string, error) {
+func (p *python3Parser) parseSingle(pyFilename string) (*treeset.Set, map[string]*treeset.Set, error) {
 	pyFilenames := treeset.NewWith(godsutils.StringComparator)
 	pyFilenames.Add(pyFilename)
 	return p.parse(pyFilenames)
@@ -109,7 +109,7 @@ func (p *python3Parser) parseSingle(pyFilename string) (*treeset.Set, []string,
 
 // parse parses multiple Python files and returns the extracted modules from
 // the import statements as well as the parsed comments.
-func (p *python3Parser) parse(pyFilenames *treeset.Set) (*treeset.Set, []string, error) {
+func (p *python3Parser) parse(pyFilenames *treeset.Set) (*treeset.Set, map[string]*treeset.Set, error) {
 	parserMutex.Lock()
 	defer parserMutex.Unlock()
 
@@ -136,10 +136,10 @@ func (p *python3Parser) parse(pyFilenames *treeset.Set) (*treeset.Set, []string,
 		return nil, nil, fmt.Errorf("failed to parse: %w", err)
 	}
 
-	var mainModules []string
+	mainModules := make(map[string]*treeset.Set, len(allRes))
 	for _, res := range allRes {
 		if res.HasMain {
-			mainModules = append(mainModules, res.FileName)
+			mainModules[res.FileName] = treeset.NewWith(moduleComparator)
 		}
 		annotations, err := annotationsFromComments(res.Comments)
 		if err != nil {
@@ -160,6 +160,9 @@ func (p *python3Parser) parse(pyFilenames *treeset.Set) (*treeset.Set, []string,
 			}
 
 			modules.Add(m)
+			if res.HasMain {
+				mainModules[res.FileName].Add(m)
+			}
 		}
 	}
 
diff --git a/gazelle/python/testdata/binary_without_entrypoint/BUILD.out b/gazelle/python/testdata/binary_without_entrypoint/BUILD.out
index 72fc670b7c..9af815286b 100644
--- a/gazelle/python/testdata/binary_without_entrypoint/BUILD.out
+++ b/gazelle/python/testdata/binary_without_entrypoint/BUILD.out
@@ -13,7 +13,10 @@ py_binary(
     name = "main",
     srcs = ["main.py"],
     visibility = ["//:__subpackages__"],
-    deps = ["@pip//:pandas"],
+    deps = [
+        ":py_default_library",
+        "@pip//:pandas",
+    ],
 )
 
 py_binary(
diff --git a/gazelle/python/testdata/binary_without_entrypoint/main.py b/gazelle/python/testdata/binary_without_entrypoint/main.py
index f13cbe58bf..f7b317062b 100644
--- a/gazelle/python/testdata/binary_without_entrypoint/main.py
+++ b/gazelle/python/testdata/binary_without_entrypoint/main.py
@@ -1,3 +1,4 @@
+import collided_main
 import pandas
 
 if __name__ == "__main__":