diff --git a/core/internal/desktop/mime.go b/core/internal/desktop/mime.go
index dde950ce1..84ffaf4fd 100644
--- a/core/internal/desktop/mime.go
+++ b/core/internal/desktop/mime.go
@@ -302,6 +302,22 @@ func AppsForMime(mimeType string) []string {
 	return out
 }
 
+// HandlersForMime lists launchable handler entries for a mime type,
+// excluding Terminal=true and NoDisplay=true desktop entries so pickers
+// only offer graphical applications.
+func HandlersForMime(mimeType string) []*Entry {
+	ids := AppsForMime(mimeType)
+	out := make([]*Entry, 0, len(ids))
+	for _, id := range ids {
+		entry := EntryByID(id)
+		if entry == nil || entry.Hidden || entry.NoDisplay || entry.Terminal {
+			continue
+		}
+		out = append(out, entry)
+	}
+	return out
+}
+
 func QueryDefaults(mimeTypes []string) map[string]string {
 	out := make(map[string]string, len(mimeTypes))
 	for _, m := range mimeTypes {
diff --git a/core/internal/desktop/mimeapps.go b/core/internal/desktop/mimeapps.go
index 6896ac72b..1feb56cb3 100644
--- a/core/internal/desktop/mimeapps.go
+++ b/core/internal/desktop/mimeapps.go
@@ -4,6 +4,7 @@ import (
 	"bufio"
 	"bytes"
 	"fmt"
+	"maps"
 	"os"
 	"path/filepath"
 	"slices"
@@ -81,7 +82,10 @@ func readAssociations(path string) (*MimeAssociations, error) {
 	if err != nil {
 		return nil, err
 	}
+	return associationsFromData(data), nil
+}
 
+func associationsFromData(data []byte) *MimeAssociations {
 	groups := parseGroups(data)
 	assoc := newAssociations()
 
@@ -106,7 +110,7 @@ func readAssociations(path string) (*MimeAssociations, error) {
 		}
 	}
 
-	return assoc, nil
+	return assoc
 }
 
 func mergedAssociations() *MimeAssociations {
@@ -144,40 +148,22 @@ func writeUserMimeapps(update func(*MimeAssociations)) error {
 
 	path := mimeappsWritePath()
 
-	assoc, err := readAssociations(path)
-	if err != nil {
-		if !os.IsNotExist(err) {
-			return err
-		}
-		assoc = newAssociations()
+	original, err := os.ReadFile(path)
+	if err != nil && !os.IsNotExist(err) {
+		return err
 	}
 
+	assoc := associationsFromData(original)
 	update(assoc)
 
-	var buf bytes.Buffer
-	w := bufio.NewWriter(&buf)
-
-	var writeErr error
-	writeSection := func(name string, entries map[string]string) {
-		fmt.Fprintf(w, "[%s]\n", name)
-		keys := make([]string, 0, len(entries))
-		for k := range entries {
-			keys = append(keys, k)
-		}
-		sort.Strings(keys)
-		for _, k := range keys {
-			v := entries[k]
-			if !isSafeIniField(k) || !isSafeIniField(v) {
-				if writeErr == nil {
-					writeErr = fmt.Errorf("invalid mimeapps.list field %q=%q", k, v)
-				}
-				continue
-			}
-			fmt.Fprintf(w, "%s=%s\n", k, v)
-		}
-		fmt.Fprintln(w)
+	rendered, err := renderMimeapps(original, assoc)
+	if err != nil {
+		return err
 	}
+	return atomicWriteFile(path, rendered)
+}
 
+func managedGroups(assoc *MimeAssociations) (map[string]map[string]string, error) {
 	flatten := func(m map[string][]string) map[string]string {
 		out := make(map[string]string, len(m))
 		for k, list := range m {
@@ -186,22 +172,172 @@ func writeUserMimeapps(update func(*MimeAssociations)) error {
 		return out
 	}
 
-	writeSection(groupDefaults, assoc.Defaults)
-	writeSection(groupAdded, flatten(assoc.Added))
-	writeSection(groupRemoved, flatten(assoc.Removed))
+	groups := map[string]map[string]string{
+		groupDefaults: maps.Clone(assoc.Defaults),
+		groupAdded:    flatten(assoc.Added),
+		groupRemoved:  flatten(assoc.Removed),
+	}
+	for name, entries := range groups {
+		for k, v := range entries {
+			if isSafeIniField(k) && isSafeIniField(v) {
+				continue
+			}
+			return nil, fmt.Errorf("invalid mimeapps.list field in [%s]: %q=%q", name, k, v)
+		}
+	}
+	return groups, nil
+}
 
-	if writeErr != nil {
-		return writeErr
+// renderMimeapps rewrites only the three association groups defined by the
+// mime-apps spec (https://specifications.freedesktop.org/mime-apps-spec/),
+// keeping comments, blank lines, and unrelated groups verbatim.
+func renderMimeapps(original []byte, assoc *MimeAssociations) ([]byte, error) {
+	managed, err := managedGroups(assoc)
+	if err != nil {
+		return nil, err
 	}
 
-	if err := w.Flush(); err != nil {
+	written := map[string]map[string]bool{
+		groupDefaults: {},
+		groupAdded:    {},
+		groupRemoved:  {},
+	}
+
+	var out []string
+
+	flushMissing := func(group string) {
+		entries, ok := managed[group]
+		if !ok {
+			return
+		}
+		keys := make([]string, 0, len(entries))
+		for k := range entries {
+			if !written[group][k] {
+				keys = append(keys, k)
+			}
+		}
+		if len(keys) == 0 {
+			return
+		}
+		sort.Strings(keys)
+
+		insertAt := len(out)
+		for insertAt > 0 && strings.TrimSpace(out[insertAt-1]) == "" {
+			insertAt--
+		}
+		lines := make([]string, 0, len(keys))
+		for _, k := range keys {
+			written[group][k] = true
+			lines = append(lines, k+"="+entries[k])
+		}
+		tail := append([]string(nil), out[insertAt:]...)
+		out = append(out[:insertAt], append(lines, tail...)...)
+	}
+
+	current := ""
+	scanner := bufio.NewScanner(bytes.NewReader(original))
+	scanner.Buffer(make([]byte, 64*1024), 1024*1024)
+	for scanner.Scan() {
+		line := scanner.Text()
+		trimmed := strings.TrimSpace(line)
+
+		if strings.HasPrefix(trimmed, "[") && strings.HasSuffix(trimmed, "]") {
+			flushMissing(current)
+			current = trimmed[1 : len(trimmed)-1]
+			out = append(out, line)
+			continue
+		}
+
+		entries, isManaged := managed[current]
+		if !isManaged {
+			out = append(out, line)
+			continue
+		}
+
+		if trimmed == "" || strings.HasPrefix(trimmed, "#") {
+			out = append(out, line)
+			continue
+		}
+
+		eq := strings.IndexByte(trimmed, '=')
+		if eq <= 0 {
+			out = append(out, line)
+			continue
+		}
+
+		key := strings.TrimSpace(trimmed[:eq])
+		val, keep := entries[key]
+		if !keep || written[current][key] {
+			continue
+		}
+		written[current][key] = true
+		out = append(out, key+"="+val)
+	}
+	if err := scanner.Err(); err != nil {
+		return nil, err
+	}
+	flushMissing(current)
+
+	for _, group := range []string{groupDefaults, groupAdded, groupRemoved} {
+		entries := managed[group]
+		pending := make([]string, 0, len(entries))
+		for k := range entries {
+			if !written[group][k] {
+				pending = append(pending, k)
+			}
+		}
+		if len(pending) == 0 {
+			continue
+		}
+		sort.Strings(pending)
+
+		if len(out) > 0 && strings.TrimSpace(out[len(out)-1]) != "" {
+			out = append(out, "")
+		}
+		out = append(out, "["+group+"]")
+		for _, k := range pending {
+			written[group][k] = true
+			out = append(out, k+"="+entries[k])
+		}
+	}
+
+	if len(out) == 0 {
+		return nil, nil
+	}
+	return []byte(strings.Join(out, "\n") + "\n"), nil
+}
+
+func atomicWriteFile(path string, data []byte) error {
+	dir := filepath.Dir(path)
+	if err := os.MkdirAll(dir, 0o755); err != nil {
 		return err
 	}
 
-	if err := os.MkdirAll(filepath.Dir(path), 0o755); err != nil {
+	tmp, err := os.CreateTemp(dir, ".mimeapps-*.tmp")
+	if err != nil {
 		return err
 	}
-	return os.WriteFile(path, buf.Bytes(), 0o644)
+	tmpPath := tmp.Name()
+
+	if _, err := tmp.Write(data); err != nil {
+		tmp.Close()
+		os.Remove(tmpPath)
+		return err
+	}
+	if err := tmp.Chmod(0o644); err != nil {
+		tmp.Close()
+		os.Remove(tmpPath)
+		return err
+	}
+	if err := tmp.Close(); err != nil {
+		os.Remove(tmpPath)
+		return err
+	}
+	if err := os.Rename(tmpPath, path); err != nil {
+		os.Remove(tmpPath)
+		return err
+	}
+	return nil
 }
 
 func setDefaultAssociation(mimeType, desktopID string) error {
diff --git a/core/internal/desktop/mimeapps_test.go b/core/internal/desktop/mimeapps_test.go
new file mode 100644
index 000000000..193c88484
--- /dev/null
+++ b/core/internal/desktop/mimeapps_test.go
@@ -0,0 +1,210 @@
+package desktop
+
+import (
+	"os"
+	"path/filepath"
+	"strings"
+	"testing"
+)
+
+func TestSetDefaultsPreservesUnrelatedContent(t *testing.T) {
+	configHome, _ := setupFakeXDG(t)
+	path := filepath.Join(configHome, "mimeapps.list")
+	writeFile(t, path, `# managed by hand
+[Default Applications]
+text/html=firefox.desktop
+# pinned image viewer
+image/png=eog.desktop
+
+[Added Associations]
+text/html=firefox.desktop;
+
+[Custom Section]
+foo=bar
+`)
+
+	if err := SetDefaults([]string{"inode/directory", "x-scheme-handler/sftp"}, "org.kde.dolphin.desktop"); err != nil {
+		t.Fatal(err)
+	}
+
+	data, err := os.ReadFile(path)
+	if err != nil {
+		t.Fatal(err)
+	}
+	got := string(data)
+
+	preserved := []string{
+		"# managed by hand",
+		"# pinned image viewer",
+		"text/html=firefox.desktop",
+		"image/png=eog.desktop",
+		"[Custom Section]",
+		"foo=bar",
+	}
+	for _, want := range preserved {
+		if !strings.Contains(got, want) {
+			t.Errorf("rewrite lost %q:\n%s", want, got)
+		}
+	}
+
+	written := []string{
+		"inode/directory=org.kde.dolphin.desktop",
+		"x-scheme-handler/sftp=org.kde.dolphin.desktop",
+	}
+	for _, want := range written {
+		if !strings.Contains(got, want) {
+			t.Errorf("rewrite missing %q:\n%s", want, got)
+		}
+	}
+
+	if got := GetDefault("inode/directory"); got != "org.kde.dolphin.desktop" {
+		t.Errorf("GetDefault(inode/directory) = %q", got)
+	}
+	if got := GetDefault("x-scheme-handler/sftp"); got != "org.kde.dolphin.desktop" {
+		t.Errorf("GetDefault(x-scheme-handler/sftp) = %q", got)
+	}
+}
+
+func TestSetDefaultReplacesKeyInPlace(t *testing.T) {
+	configHome, _ := setupFakeXDG(t)
+	path := filepath.Join(configHome, "mimeapps.list")
+	writeFile(t, path, `[Default Applications]
+inode/directory=foot.desktop
+text/html=firefox.desktop
+`)
+
+	if err := SetDefault("inode/directory", "org.gnome.Nautilus.desktop"); err != nil {
+		t.Fatal(err)
+	}
+
+	data, err := os.ReadFile(path)
+	if err != nil {
+		t.Fatal(err)
+	}
+	got := string(data)
+
+	if n := strings.Count(got, "inode/directory=org.gnome.Nautilus.desktop\n"); n != 1 {
+		t.Errorf("expected exactly one replaced default line, got %d:\n%s", n, got)
+	}
+	if strings.Contains(got, "foot.desktop") {
+		t.Errorf("old default still present:\n%s", got)
+	}
+	if !strings.Contains(got, "text/html=firefox.desktop") {
+		t.Errorf("unrelated default lost:\n%s", got)
+	}
+}
+
+func TestSetDefaultsCreatesFileWhenAbsent(t *testing.T) {
+	configHome, _ := setupFakeXDG(t)
+	path := filepath.Join(configHome, "mimeapps.list")
+
+	if err := SetDefaults([]string{"inode/directory", "x-scheme-handler/sftp"}, "org.kde.dolphin"); err != nil {
+		t.Fatal(err)
+	}
+
+	data, err := os.ReadFile(path)
+	if err != nil {
+		t.Fatal(err)
+	}
+	got := string(data)
+
+	expected := []string{
+		"[Default Applications]",
+		"inode/directory=org.kde.dolphin.desktop",
+		"x-scheme-handler/sftp=org.kde.dolphin.desktop",
+		"[Added Associations]",
+	}
+	for _, want := range expected {
+		if !strings.Contains(got, want) {
+			t.Errorf("new file missing %q:\n%s", want, got)
+		}
+	}
+
+	entries, err := os.ReadDir(configHome)
+	if err != nil {
+		t.Fatal(err)
+	}
+	for _, e := range entries {
+		if strings.HasSuffix(e.Name(), ".tmp") {
+			t.Errorf("leftover temp file %q", e.Name())
+		}
+	}
+}
+
+func TestSetDefaultClearsRemovedAssociation(t *testing.T) {
+	configHome, _ := setupFakeXDG(t)
+	path := filepath.Join(configHome, "mimeapps.list")
+	writeFile(t, path, `[Removed Associations]
+inode/directory=org.kde.dolphin.desktop;other.desktop;
+`)
+
+	if err := SetDefault("inode/directory", "org.kde.dolphin.desktop"); err != nil {
+		t.Fatal(err)
+	}
+
+	data, err := os.ReadFile(path)
+	if err != nil {
+		t.Fatal(err)
+	}
+	got := string(data)
+
+	if !strings.Contains(got, "inode/directory=other.desktop;") {
+		t.Errorf("unrelated removed entry lost:\n%s", got)
+	}
+	if strings.Contains(got, "org.kde.dolphin.desktop;other.desktop") {
+		t.Errorf("chosen app still in removed list:\n%s", got)
+	}
+	if got := GetDefault("inode/directory"); got != "org.kde.dolphin.desktop" {
+		t.Errorf("GetDefault = %q", got)
+	}
+}
+
+func TestHandlersForMimeExcludesTerminalAndNoDisplay(t *testing.T) {
+	_, dataHome := setupFakeXDG(t)
+	apps := filepath.Join(dataHome, "applications")
+	writeFile(t, filepath.Join(apps, "org.kde.dolphin.desktop"), `[Desktop Entry]
+Type=Application
+Name=Dolphin
+Icon=system-file-manager
+MimeType=inode/directory;
+`)
+	writeFile(t, filepath.Join(apps, "ghost-term.desktop"), `[Desktop Entry]
+Type=Application
+Name=Ghost Terminal
+Terminal=true
+MimeType=inode/directory;
+`)
+	writeFile(t, filepath.Join(apps, "hidden-fm.desktop"), `[Desktop Entry]
+Type=Application
+Name=Hidden FM
+NoDisplay=true
+MimeType=inode/directory;
+`)
+	writeFile(t, filepath.Join(apps, "mimeinfo.cache"), `[MIME Cache]
+inode/directory=ghost-term.desktop;org.kde.dolphin.desktop;hidden-fm.desktop;stale.desktop;
+`)
+
+	handlers := HandlersForMime("inode/directory")
+	byID := make(map[string]*Entry, len(handlers))
+	for _, h := range handlers {
+		byID[h.ID] = h
+	}
+
+	dolphin := byID["org.kde.dolphin.desktop"]
+	if dolphin == nil {
+		t.Fatal("org.kde.dolphin.desktop missing from handlers")
+	}
+	if dolphin.Name != "Dolphin" {
+		t.Errorf("Name = %q", dolphin.Name)
+	}
+	if dolphin.Icon != "system-file-manager" {
+		t.Errorf("Icon = %q", dolphin.Icon)
+	}
+
+	excluded := []string{"ghost-term.desktop", "hidden-fm.desktop", "stale.desktop"}
+	for _, id := range excluded {
+		if byID[id] != nil {
+			t.Errorf("%s should be excluded from handlers", id)
+		}
+	}
+}
diff --git a/core/internal/server/mime/handlers.go b/core/internal/server/mime/handlers.go
index 4c58c51ed..ab195c90f 100644
--- a/core/internal/server/mime/handlers.go
+++ b/core/internal/server/mime/handlers.go
@@ -18,6 +18,17 @@ type appsResult struct {
 	DesktopIDs []string `json:"desktopIds"`
 }
 
+type handlerApp struct {
+	ID   string `json:"id"`
+	Name string `json:"name"`
+	Icon string `json:"icon,omitempty"`
+}
+
+type handlersResult struct {
+	MimeType string       `json:"mimeType"`
+	Apps     []handlerApp `json:"apps"`
+}
+
 type queryResult struct {
 	Defaults map[string]string `json:"defaults"`
 }
@@ -32,6 +43,8 @@ func HandleRequest(conn *models.Conn, req models.Request) {
 		handleSetDefaults(conn, req)
 	case "mime.appsForMime":
 		handleAppsForMime(conn, req)
+	case "mime.handlersForMime":
+		handleHandlersForMime(conn, req)
 	case "mime.queryDefaults":
 		handleQueryDefaults(conn, req)
 	case "mime.invalidate":
@@ -106,6 +119,27 @@ func handleAppsForMime(conn *models.Conn, req models.Request) {
 	})
 }
 
+func handleHandlersForMime(conn *models.Conn, req models.Request) {
+	mimeType, err := mimeParam(req.Params, "mimeType")
+	if err != nil {
+		models.RespondError(conn, req.ID, err.Error())
+		return
+	}
+	entries := desktop.HandlersForMime(mimeType)
+	apps := make([]handlerApp, 0, len(entries))
+	for _, entry := range entries {
+		apps = append(apps, handlerApp{
+			ID:   entry.ID,
+			Name: entry.Name,
+			Icon: entry.Icon,
+		})
+	}
+	models.Respond(conn, req.ID, handlersResult{
+		MimeType: mimeType,
+		Apps:     apps,
+	})
+}
+
 func handleQueryDefaults(conn *models.Conn, req models.Request) {
 	mimeTypes, err := mimeListParam(req, "mimeTypes")
 	if err != nil {
diff --git a/quickshell/Modules/Settings/DefaultAppsTab.qml b/quickshell/Modules/Settings/DefaultAppsTab.qml
index 73894aa9d..aa5920fd3 100644
--- a/quickshell/Modules/Settings/DefaultAppsTab.qml
+++ b/quickshell/Modules/Settings/DefaultAppsTab.qml
@@ -42,7 +42,7 @@ Item {
     // the rest are for setting the default app.
     readonly property var mimeMapping: ({
             [root.appCategory.WebBrowser]: ["x-scheme-handler/https", "x-scheme-handler/http", "text/html", "application/xhtml+xml"],
-            [root.appCategory.FileManager]: ["inode/directory", "x-scheme-handler/file"],
+            [root.appCategory.FileManager]: ["inode/directory", "x-scheme-handler/file", "x-scheme-handler/sftp"],
             [root.appCategory.TextEditor]: ["text/plain", "text/markdown", "application/x-zerosize", "text/x-c++src", "text/x-csrc", "text/x-python", "text/x-shellscript", "application/json"],
             [root.appCategory.ImageViewer]: ["image/png", "image/jpeg", "image/gif", "image/bmp", "image/webp", "image/avif", "image/svg+xml"],
             [root.appCategory.VideoPlayer]: ["video/mp4", "video/x-matroska", "video/webm", "video/avi", "video/mpeg", "video/quicktime", "video/x-msvideo"],
@@ -131,6 +131,7 @@ Item {
                 // you don't want Kate as your file manager just because it can open folders
                 loadCategoryModel(root.appCategory.FileManager, "FileManager");
                 DesktopService.getDefaultApp(mimeMapping[category][0], category.toString());
+                DesktopService.getHandlersForMimeType(mimeMapping[category][0], category.toString());
                 break;
             default:
                 const mimeType = mimeMapping[category][0];
@@ -216,6 +217,22 @@ Item {
             root.categoryModels = models;
         }
 
+        function onGetHandlersForMimeResult(mimeType, apps, callbackId) {
+            const categoryIndex = parseInt(callbackId);
+            let models = Object.assign({}, root.categoryModels);
+            const existing = models[categoryIndex] || root.withDmsChooser([]);
+            const known = new Set(existing.map(opt => opt.value));
+            const extra = (apps || []).filter(app => app.id && !known.has(app.id)).map(app => ({
+                        text: app.name || root.getAppDisplayName(app.id),
+                        value: app.id
+                    }));
+            if (extra.length === 0) {
+                return;
+            }
+            models[categoryIndex] = existing.concat(extra);
+            root.categoryModels = models;
+        }
+
         function onGetDefaultAppResult(mimeType, desktopFileId, callbackId) {
             if (!desktopFileId) {
                 log.info("No default app found for MIME type:", mimeType);
@@ -302,7 +319,7 @@ Item {
 
                 AppSelector {
                     text: I18n.tr("File Manager", "File Manager")
-                    tags: ["file", "manager"]
+                    tags: ["file", "manager", "directory", "sftp"]
                     category: root.appCategory.FileManager
                     description: I18n.tr("Manages files and directories", "Manages files and directories")
                 }
diff --git a/quickshell/Services/DesktopService.qml b/quickshell/Services/DesktopService.qml
index 23b832655..64b1dc94c 100644
--- a/quickshell/Services/DesktopService.qml
+++ b/quickshell/Services/DesktopService.qml
@@ -127,6 +127,7 @@ Singleton {
 
     signal getDefaultAppResult(string mimeType, string desktopFileId, string callbackId)
     signal getAppsForMimeResult(string mimeType, var appIds, string callbackId)
+    signal getHandlersForMimeResult(string mimeType, var apps, string callbackId)
 
     function setDefaultApp(mimeType, desktopFileId, callbackId = "") {
         setDefaultAppForMimes([mimeType], desktopFileId, callbackId);
@@ -162,6 +163,19 @@ Singleton {
         });
     }
 
+    function getHandlersForMimeType(mimeType, callbackId = "") {
+        DMSService.sendRequest("mime.handlersForMime", {
+            "mimeType": mimeType
+        }, response => {
+            if (response.error) {
+                log.warn("DesktopService.getHandlersForMimeType failed:", response.error, "mime:", mimeType);
+                return;
+            }
+            const result = response.result || {};
+            root.getHandlersForMimeResult(mimeType, result.apps || [], callbackId);
+        });
+    }
+
     function getAppsForMimeType(mimeType, callbackId = "") {
         DMSService.sendRequest("mime.appsForMime", {
             "mimeType": mimeType