diff --git a/commands/command_clone.go b/commands/command_clone.go
index a2db0ce9..1d354dcb 100644
--- a/commands/command_clone.go
+++ b/commands/command_clone.go
@@ -79,7 +79,7 @@ func cloneCommand(cmd *cobra.Command, args []string) {
 
 	if ref, err := git.CurrentRef(); err == nil {
 		includeArg, excludeArg := getIncludeExcludeArgs(cmd)
-		filter := buildFilepathFilter(cfg, includeArg, excludeArg)
+		filter := buildFilepathFilter(cfg, includeArg, excludeArg, true)
 		if cloneFlags.NoCheckout || cloneFlags.Bare {
 			// If --no-checkout or --bare then we shouldn't check out, just fetch instead
 			fetchRef(ref.Name, filter)
diff --git a/commands/command_fetch.go b/commands/command_fetch.go
index a36a1014..ed0f197a 100644
--- a/commands/command_fetch.go
+++ b/commands/command_fetch.go
@@ -88,7 +88,7 @@ func fetchCommand(cmd *cobra.Command, args []string) {
 		}
 
 	} else { // !all
-		filter := buildFilepathFilter(cfg, include, exclude)
+		filter := buildFilepathFilter(cfg, include, exclude, true)
 
 		// Fetch refs sequentially per arg order; duplicates in later refs will be ignored
 		for _, ref := range refs {
diff --git a/commands/command_ls_files.go b/commands/command_ls_files.go
index eee5ad9e..75f244ef 100644
--- a/commands/command_ls_files.go
+++ b/commands/command_ls_files.go
@@ -107,7 +107,7 @@ func lsFilesCommand(cmd *cobra.Command, args []string) {
 	defer gitscanner.Close()
 
 	includeArg, excludeArg := getIncludeExcludeArgs(cmd)
-	gitscanner.Filter = buildFilepathFilter(cfg, includeArg, excludeArg)
+	gitscanner.Filter = buildFilepathFilter(cfg, includeArg, excludeArg, false)
 
 	if len(args) == 0 {
 		// Only scan the index when "git lfs ls-files" was invoked with
diff --git a/commands/command_migrate.go b/commands/command_migrate.go
index 6b534d2d..ea362d8a 100644
--- a/commands/command_migrate.go
+++ b/commands/command_migrate.go
@@ -303,7 +303,7 @@ func currentRefToMigrate() (*git.Ref, error) {
 // filter given by the --include and --exclude arguments.
 func getHistoryRewriter(cmd *cobra.Command, db *gitobj.ObjectDatabase, l *tasklog.Logger) *githistory.Rewriter {
 	include, exclude := getIncludeExcludeArgs(cmd)
-	filter := buildFilepathFilter(cfg, include, exclude)
+	filter := buildFilepathFilter(cfg, include, exclude, false)
 
 	return githistory.NewRewriter(db,
 		githistory.WithFilter(filter), githistory.WithLogger(l))
diff --git a/commands/command_pull.go b/commands/command_pull.go
index a20dbd52..9cdacb18 100644
--- a/commands/command_pull.go
+++ b/commands/command_pull.go
@@ -27,7 +27,7 @@ func pullCommand(cmd *cobra.Command, args []string) {
 	}
 
 	includeArg, excludeArg := getIncludeExcludeArgs(cmd)
-	filter := buildFilepathFilter(cfg, includeArg, excludeArg)
+	filter := buildFilepathFilter(cfg, includeArg, excludeArg, true)
 	pull(filter)
 }
 
diff --git a/commands/commands.go b/commands/commands.go
index 365be88d..e612a1b3 100644
--- a/commands/commands.go
+++ b/commands/commands.go
@@ -126,8 +126,8 @@ func currentRemoteRef() *git.Ref {
 	return git.NewRefUpdate(cfg.Git, cfg.PushRemote(), cfg.CurrentRef(), nil).Right()
 }
 
-func buildFilepathFilter(config *config.Configuration, includeArg, excludeArg *string) *filepathfilter.Filter {
-	inc, exc := determineIncludeExcludePaths(config, includeArg, excludeArg)
+func buildFilepathFilter(config *config.Configuration, includeArg, excludeArg *string, useFetchOptions bool) *filepathfilter.Filter {
+	inc, exc := determineIncludeExcludePaths(config, includeArg, excludeArg, useFetchOptions)
 	return filepathfilter.New(inc, exc)
 }
 
@@ -449,14 +449,22 @@ func logPanicToWriter(w io.Writer, loggedError error, le string) {
 	}
 }
 
-func determineIncludeExcludePaths(config *config.Configuration, includeArg, excludeArg *string) (include, exclude []string) {
+func determineIncludeExcludePaths(config *config.Configuration, includeArg, excludeArg *string, useFetchOptions bool) (include, exclude []string) {
 	if includeArg == nil {
-		include = config.FetchIncludePaths()
+		if useFetchOptions {
+			include = config.FetchIncludePaths()
+		} else {
+			include = []string{}
+		}
 	} else {
 		include = tools.CleanPaths(*includeArg, ",")
 	}
 	if excludeArg == nil {
-		exclude = config.FetchExcludePaths()
+		if useFetchOptions {
+			exclude = config.FetchExcludePaths()
+		} else {
+			exclude = []string{}
+		}
 	} else {
 		exclude = tools.CleanPaths(*excludeArg, ",")
 	}
diff --git a/commands/commands_test.go b/commands/commands_test.go
index b0b91b95..596ab038 100644
--- a/commands/commands_test.go
+++ b/commands/commands_test.go
@@ -19,7 +19,7 @@ var (
 func TestDetermineIncludeExcludePathsReturnsCleanedPaths(t *testing.T) {
 	inc := "/some/include"
 	exc := "/some/exclude"
-	i, e := determineIncludeExcludePaths(testcfg, &inc, &exc)
+	i, e := determineIncludeExcludePaths(testcfg, &inc, &exc, true)
 
 	assert.Equal(t, []string{"/some/include"}, i)
 	assert.Equal(t, []string{"/some/exclude"}, e)
@@ -28,15 +28,22 @@ func TestDetermineIncludeExcludePathsReturnsCleanedPaths(t *testing.T) {
 func TestDetermineIncludeExcludePathsReturnsEmptyPaths(t *testing.T) {
 	inc := ""
 	exc := ""
-	i, e := determineIncludeExcludePaths(testcfg, &inc, &exc)
+	i, e := determineIncludeExcludePaths(testcfg, &inc, &exc, true)
 
 	assert.Empty(t, i)
 	assert.Empty(t, e)
 }
 
 func TestDetermineIncludeExcludePathsReturnsDefaultsWhenAbsent(t *testing.T) {
-	i, e := determineIncludeExcludePaths(testcfg, nil, nil)
+	i, e := determineIncludeExcludePaths(testcfg, nil, nil, true)
 
 	assert.Equal(t, []string{"/default/include"}, i)
 	assert.Equal(t, []string{"/default/exclude"}, e)
 }
+
+func TestDetermineIncludeExcludePathsReturnsNothingWhenAbsent(t *testing.T) {
+	i, e := determineIncludeExcludePaths(testcfg, nil, nil, false)
+
+	assert.Empty(t, i)
+	assert.Empty(t, e)
+}
diff --git a/t/t-ls-files.sh b/t/t-ls-files.sh
index 360f7b5a..143ba63b 100755
--- a/t/t-ls-files.sh
+++ b/t/t-ls-files.sh
@@ -497,4 +497,22 @@ begin_test "ls-files: history with reference range"
   [ 0 -eq $(grep -c "b\.dat" ls-files.log) ]
   [ 0 -eq $(grep -c "c\.dat" ls-files.log) ]
 )
+end_test
+
+begin_test "ls-files: not affected by lfs.fetchexclude"
+(
+  set -e
+
+  mkdir repo-fetchexclude
+  cd repo-fetchexclude
+  git init
+  git lfs track "*.dat" | grep "Tracking \"\*.dat\""
+  echo "some data" > some.dat
+  echo "some text" > some.txt
+  echo "missing" > missing.dat
+  git add missing.dat
+  git commit -m "add missing file"
+  git config lfs.fetchexclude '*'
+  [ "6bbd052ab0 * missing.dat" = "$(git lfs ls-files)" ]
+)
 end_test
\ No newline at end of file