diff --git a/internal/git/exec.go b/internal/git/exec.go
index 91ae864e..19012958 100644
--- a/internal/git/exec.go
+++ b/internal/git/exec.go
@@ -3,6 +3,7 @@ package git
 import (
 	"os"
 	"os/exec"
+	"path/filepath"
 	"strings"
 
 	"github.com/evilmartians/lefthook/internal/log"
@@ -12,6 +13,7 @@ type Exec interface {
 	SetRootPath(root string)
 	Cmd(cmd []string) (string, error)
 	CmdLines(cmd []string) ([]string, error)
+	CmdLinesWithinFolder(cmd []string, folder string) ([]string, error)
 }
 
 type OsExec struct {
@@ -30,7 +32,7 @@ func (o *OsExec) SetRootPath(root string) {
 
 // Cmd runs plain string command. Trims spaces around output.
 func (o *OsExec) Cmd(cmd []string) (string, error) {
-	out, err := o.rawExecArgs(cmd)
+	out, err := o.rawExecArgs(cmd, "")
 	if err != nil {
 		return "", err
 	}
@@ -40,7 +42,17 @@ func (o *OsExec) Cmd(cmd []string) (string, error) {
 
 // CmdLines runs plain string command, returns its output split by newline.
 func (o *OsExec) CmdLines(cmd []string) ([]string, error) {
-	out, err := o.rawExecArgs(cmd)
+	out, err := o.rawExecArgs(cmd, "")
+	if err != nil {
+		return nil, err
+	}
+
+	return strings.Split(strings.TrimSpace(out), "\n"), nil
+}
+
+// CmdLines runs plain string command, returns its output split by newline.
+func (o *OsExec) CmdLinesWithinFolder(cmd []string, folder string) ([]string, error) {
+	out, err := o.rawExecArgs(cmd, folder)
 	if err != nil {
 		return nil, err
 	}
@@ -50,15 +62,16 @@ func (o *OsExec) CmdLines(cmd []string) ([]string, error) {
 
 // rawExecArgs executes git command with LEFTHOOK=0 in order
 // to prevent calling subsequent lefthook hooks.
-func (o *OsExec) rawExecArgs(args []string) (string, error) {
+func (o *OsExec) rawExecArgs(args []string, folder string) (string, error) {
 	log.Debug("[lefthook] cmd: ", args)
 
+	root := filepath.Join(o.root, folder)
 	cmd := exec.Command(args[0], args[1:]...)
-	cmd.Dir = o.root
+	cmd.Dir = root
 	cmd.Env = append(os.Environ(), "LEFTHOOK=0")
 
 	out, err := cmd.CombinedOutput()
-	log.Debug("[lefthook] dir: ", o.root)
+	log.Debug("[lefthook] dir: ", root)
 	log.Debug("[lefthook] err: ", err)
 	log.Debug("[lefthook] out: ", string(out))
 	if err != nil {
diff --git a/internal/git/repository.go b/internal/git/repository.go
index aa92adac..01901d2b 100644
--- a/internal/git/repository.go
+++ b/internal/git/repository.go
@@ -108,19 +108,19 @@ func NewRepository(fs afero.Fs, git Exec) (*Repository, error) {
 // StagedFiles returns a list of staged files
 // or an error if git command fails.
 func (r *Repository) StagedFiles() ([]string, error) {
-	return r.FilesByCommand(cmdStagedFiles)
+	return r.FilesByCommand(cmdStagedFiles, "")
 }
 
 // StagedFiles returns a list of all files in repository
 // or an error if git command fails.
 func (r *Repository) AllFiles() ([]string, error) {
-	return r.FilesByCommand(cmdAllFiles)
+	return r.FilesByCommand(cmdAllFiles, "")
 }
 
 // PushFiles returns a list of files that are ready to be pushed
 // or an error if git command fails.
 func (r *Repository) PushFiles() ([]string, error) {
-	res, err := r.FilesByCommand(cmdPushFilesBase)
+	res, err := r.FilesByCommand(cmdPushFilesBase, "")
 	if err == nil {
 		return res, nil
 	}
@@ -147,7 +147,7 @@ func (r *Repository) PushFiles() ([]string, error) {
 		r.headBranch = r.emptyTreeSHA
 	}
 
-	return r.FilesByCommand(append(cmdPushFilesHead, r.headBranch))
+	return r.FilesByCommand(append(cmdPushFilesHead, r.headBranch), "")
 }
 
 // PartiallyStagedFiles returns the list of files that have both staged and
@@ -319,8 +319,8 @@ func (r *Repository) AddFiles(files []string) error {
 }
 
 // FilesByCommand accepts git command and returns its result as a list of filepaths.
-func (r *Repository) FilesByCommand(command []string) ([]string, error) {
-	lines, err := r.Git.CmdLines(command)
+func (r *Repository) FilesByCommand(command []string, folder string) ([]string, error) {
+	lines, err := r.Git.CmdLinesWithinFolder(command, folder)
 	if err != nil {
 		return nil, err
 	}
diff --git a/internal/git/repository_test.go b/internal/git/repository_test.go
index ea2be416..68f77369 100644
--- a/internal/git/repository_test.go
+++ b/internal/git/repository_test.go
@@ -31,6 +31,10 @@ func (g GitMock) CmdLines(cmd []string) ([]string, error) {
 	return strings.Split(res, "\n"), nil
 }
 
+func (g GitMock) CmdLinesWithinFolder(cmd []string, _folder string) ([]string, error) {
+	return g.CmdLines(cmd)
+}
+
 func TestPartiallyStagedFiles(t *testing.T) {
 	for i, tt := range [...]struct {
 		name, gitOut string
diff --git a/internal/lefthook/run_test.go b/internal/lefthook/run_test.go
index ac6b7f1b..fd8b2da5 100644
--- a/internal/lefthook/run_test.go
+++ b/internal/lefthook/run_test.go
@@ -23,6 +23,10 @@ func (g GitMock) CmdLines(_cmd []string) ([]string, error) {
 	return nil, nil
 }
 
+func (g GitMock) CmdLinesWithinFolder(_cmd []string, _folder string) ([]string, error) {
+	return nil, nil
+}
+
 func TestRun(t *testing.T) {
 	root, err := filepath.Abs("src")
 	if err != nil {
diff --git a/internal/lefthook/runner/prepare_command.go b/internal/lefthook/runner/prepare_command.go
index f021a37a..09b6a36b 100644
--- a/internal/lefthook/runner/prepare_command.go
+++ b/internal/lefthook/runner/prepare_command.go
@@ -88,7 +88,7 @@ func (r *Runner) buildRun(command *config.Command) (*run, error) {
 			} else {
 				cmd = []string{"sh", "-c", filesCmd}
 			}
-			return r.Repo.FilesByCommand(cmd)
+			return r.Repo.FilesByCommand(cmd, command.Root)
 		}
 	}
 
diff --git a/internal/lefthook/runner/runner_test.go b/internal/lefthook/runner/runner_test.go
index 0c427754..41e8ee0c 100644
--- a/internal/lefthook/runner/runner_test.go
+++ b/internal/lefthook/runner/runner_test.go
@@ -68,6 +68,10 @@ func (g *GitMock) CmdLines(args []string) ([]string, error) {
 	return nil, nil
 }
 
+func (g *GitMock) CmdLinesWithinFolder(args []string, _folder string) ([]string, error) {
+	return g.CmdLines(args)
+}
+
 func (g *GitMock) reset() {
 	g.mux.Lock()
 	g.commands = []string{}