diff --git a/knotserver/git/merge.go b/knotserver/git/merge.go
index aa9edb5a..9057650d 100644
--- a/knotserver/git/merge.go
+++ b/knotserver/git/merge.go
@@ -31,6 +31,7 @@ type MergeOptions struct {
 	CommitBody    string
 	AuthorName    string
 	AuthorEmail   string
+	FormatPatch   bool
 }
 
 func (e ErrMerge) Error() string {
@@ -86,17 +87,12 @@ func (g *GitRepo) cloneRepository(targetBranch string) (string, error) {
 func (g *GitRepo) applyPatch(tmpDir, patchFile string, checkOnly bool, opts *MergeOptions) error {
 	var stderr bytes.Buffer
 	var cmd *exec.Cmd
-	var formatPatch = false
-
-	if patchutil.IsFormatPatch(patchFile) {
-		formatPatch = true
-	}
 
 	if checkOnly {
 		cmd = exec.Command("git", "-C", tmpDir, "apply", "--check", "-v", patchFile)
 	} else {
 		// if patch is a format-patch, apply using 'git am'
-		if formatPatch {
+		if opts.FormatPatch {
 			amCmd := exec.Command("git", "-C", tmpDir, "am", patchFile)
 			amCmd.Stderr = &stderr
 			if err := amCmd.Run(); err != nil {
@@ -169,6 +165,9 @@ func (g *GitRepo) applyPatch(tmpDir, patchFile string, checkOnly bool, opts *Mer
 }
 
 func (g *GitRepo) MergeCheck(patchData []byte, targetBranch string) error {
+	var opts MergeOptions
+	opts.FormatPatch = patchutil.IsFormatPatch(string(patchData))
+
 	patchFile, err := g.createTempFileWithPatch(patchData)
 	if err != nil {
 		return &ErrMerge{
@@ -187,7 +186,7 @@ func (g *GitRepo) MergeCheck(patchData []byte, targetBranch string) error {
 	}
 	defer os.RemoveAll(tmpDir)
 
-	return g.applyPatch(tmpDir, patchFile, true, nil)
+	return g.applyPatch(tmpDir, patchFile, true, &opts)
 }
 
 func (g *GitRepo) Merge(patchData []byte, targetBranch string) error {
diff --git a/knotserver/routes.go b/knotserver/routes.go
index a2a1dc3e..33408b0d 100644
--- a/knotserver/routes.go
+++ b/knotserver/routes.go
@@ -24,6 +24,7 @@ import (
 	"github.com/go-git/go-git/v5/plumbing/object"
 	"tangled.sh/tangled.sh/core/knotserver/db"
 	"tangled.sh/tangled.sh/core/knotserver/git"
+	"tangled.sh/tangled.sh/core/patchutil"
 	"tangled.sh/tangled.sh/core/types"
 )
 
@@ -687,6 +688,9 @@ func (h *Handle) Merge(w http.ResponseWriter, r *http.Request) {
 		notFound(w)
 		return
 	}
+
+	mo.FormatPatch = patchutil.IsFormatPatch(patch)
+
 	if err := gr.MergeWithOptions([]byte(patch), branch, mo); err != nil {
 		var mergeErr *git.ErrMerge
 		if errors.As(err, &mergeErr) {