diff --git a/gazelle/python/configure.go b/gazelle/python/configure.go
index ed6e2e102c..4ae4c23b3f 100644
--- a/gazelle/python/configure.go
+++ b/gazelle/python/configure.go
@@ -90,11 +90,11 @@ func (py *Configurer) Configure(c *config.Config, rel string, f *rule.File) {
 
 	configs := c.Exts[languageName].(pythonconfig.Configs)
 
-	config, exists := configs[rel]
+	config, exists := configs[filepath.FromSlash(rel)]
 	if !exists {
 		parent := configs.ParentForPackage(rel)
 		config = parent.NewChild()
-		configs[rel] = config
+		configs[filepath.FromSlash(rel)] = config
 	}
 
 	if f == nil {
diff --git a/gazelle/python/generate.go b/gazelle/python/generate.go
index 1937831c44..786baf3ce9 100644
--- a/gazelle/python/generate.go
+++ b/gazelle/python/generate.go
@@ -70,7 +70,7 @@ func matchesAnyGlob(s string, globs []string) bool {
 // in depth-first post-order.
 func (py *Python) GenerateRules(args language.GenerateArgs) language.GenerateResult {
 	cfgs := args.Config.Exts[languageName].(pythonconfig.Configs)
-	cfg := cfgs[args.Rel]
+	cfg := cfgs[filepath.FromSlash(args.Rel)]
 
 	if !cfg.ExtensionEnabled() {
 		return language.GenerateResult{}
diff --git a/gazelle/python/resolve.go b/gazelle/python/resolve.go
index f019a64c1a..63372213f8 100644
--- a/gazelle/python/resolve.go
+++ b/gazelle/python/resolve.go
@@ -56,7 +56,7 @@ func (*Resolver) Name() string { return languageName }
 // returned, including an empty slice, the rule will be indexed.
 func (py *Resolver) Imports(c *config.Config, r *rule.Rule, f *rule.File) []resolve.ImportSpec {
 	cfgs := c.Exts[languageName].(pythonconfig.Configs)
-	cfg := cfgs[f.Pkg]
+	cfg := cfgs[filepath.FromSlash(f.Pkg)]
 	srcs := r.AttrStrings("srcs")
 	provides := make([]resolve.ImportSpec, 0, len(srcs)+1)
 	for _, src := range srcs {
@@ -143,7 +143,7 @@ func (py *Resolver) Resolve(
 	deps := treeset.NewWith(godsutils.StringComparator)
 	if modulesRaw != nil {
 		cfgs := c.Exts[languageName].(pythonconfig.Configs)
-		cfg := cfgs[from.Pkg]
+		cfg := cfgs[filepath.FromSlash(from.Pkg)]
 		pythonProjectRoot := cfg.PythonProjectRoot()
 		modules := modulesRaw.(*treeset.Set)
 		it := modules.Iterator()