diff --git a/apps/desktop/src/app/utils/navigation.ts b/apps/desktop/src/app/utils/navigation.ts
index f6c94933..fc996ad6 100644
--- a/apps/desktop/src/app/utils/navigation.ts
+++ b/apps/desktop/src/app/utils/navigation.ts
@@ -1,4 +1,6 @@
 export const REVEAL_NOTE_IN_TREE_EVENT = "neverwrite:reveal-note-in-tree";
+export const CLEAR_FILE_TREE_SELECTION_EVENT =
+    "neverwrite:clear-file-tree-selection";
 
 export function revealNoteInTree(noteId: string) {
     window.dispatchEvent(
@@ -7,3 +9,7 @@ export function revealNoteInTree(noteId: string) {
         }),
     );
 }
+
+export function clearFileTreeSelection() {
+    window.dispatchEvent(new CustomEvent(CLEAR_FILE_TREE_SELECTION_EVENT));
+}
diff --git a/apps/desktop/src/features/editor/MultiPaneWorkspace.test.tsx b/apps/desktop/src/features/editor/MultiPaneWorkspace.test.tsx
index a4f3e90d..008be4d5 100644
--- a/apps/desktop/src/features/editor/MultiPaneWorkspace.test.tsx
+++ b/apps/desktop/src/features/editor/MultiPaneWorkspace.test.tsx
@@ -10,6 +10,7 @@ import {
 } from "../../test/test-utils";
 import { publishWindowTabDropZone } from "../../app/detachedWindows";
 import { useEditorStore } from "../../app/store/editorStore";
+import { CLEAR_FILE_TREE_SELECTION_EVENT } from "../../app/utils/navigation";
 import {
     createInitialLayout,
     splitPane,
@@ -223,6 +224,33 @@ describe("MultiPaneWorkspace", () => {
         expect(useEditorStore.getState().focusedPaneId).toBe("secondary");
     });
 
+    it("requests file tree selection cleanup when a pane is clicked", () => {
+        const events: Event[] = [];
+        const handleClearSelection = (event: Event) => events.push(event);
+        window.addEventListener(
+            CLEAR_FILE_TREE_SELECTION_EVENT,
+            handleClearSelection,
+        );
+
+        try {
+            renderComponent(<MultiPaneWorkspace />);
+
+            const targetPane = screen
+                .getByTestId("pane-content-secondary")
+                .closest('[data-editor-pane-id="secondary"]');
+            expect(targetPane).not.toBeNull();
+
+            fireEvent.pointerDown(targetPane!, { pointerId: 1, button: 0 });
+
+            expect(events).toHaveLength(1);
+        } finally {
+            window.removeEventListener(
+                CLEAR_FILE_TREE_SELECTION_EVENT,
+                handleClearSelection,
+            );
+        }
+    });
+
     it("opens a dragged vault file in the pane under the pointer", async () => {
         setVaultEntries([
             {
diff --git a/apps/desktop/src/features/editor/MultiPaneWorkspace.tsx b/apps/desktop/src/features/editor/MultiPaneWorkspace.tsx
index 83fa7672..d7b5b275 100644
--- a/apps/desktop/src/features/editor/MultiPaneWorkspace.tsx
+++ b/apps/desktop/src/features/editor/MultiPaneWorkspace.tsx
@@ -13,6 +13,7 @@ import {
     getCurrentWindowLabel,
     publishWindowTabDropZone,
 } from "../../app/detachedWindows";
+import { clearFileTreeSelection } from "../../app/utils/navigation";
 import {
     selectFocusedPaneId,
     selectLeafPaneIds,
@@ -382,6 +383,10 @@ export function MultiPaneWorkspace() {
         [focusPane],
     );
 
+    const handlePanePointerDown = useCallback(() => {
+        clearFileTreeSelection();
+    }, []);
+
     const handleResizeSplit = useCallback(
         (splitId: string, sizes: readonly number[]) => {
             resizePaneSplit(splitId, sizes);
@@ -578,6 +583,7 @@ export function MultiPaneWorkspace() {
                 node={layoutTree}
                 focusedPaneId={focusedPaneId}
                 externalFileDropPaneId={externalFileDropPaneId}
+                onPanePointerDown={handlePanePointerDown}
                 onPaneFocus={handlePaneFocus}
                 onResizeSplit={handleResizeSplit}
             />
diff --git a/apps/desktop/src/features/editor/WorkspaceSplitContainer.tsx b/apps/desktop/src/features/editor/WorkspaceSplitContainer.tsx
index 78066cc6..b1a7dcd2 100644
--- a/apps/desktop/src/features/editor/WorkspaceSplitContainer.tsx
+++ b/apps/desktop/src/features/editor/WorkspaceSplitContainer.tsx
@@ -36,6 +36,7 @@ interface WorkspaceSplitContainerProps {
     node: WorkspaceLayoutNode;
     focusedPaneId: string | null;
     externalFileDropPaneId: string | null;
+    onPanePointerDown: () => void;
     onPaneFocus: (paneId: string) => void;
     onResizeSplit: (splitId: string, sizes: readonly number[]) => void;
 }
@@ -94,11 +95,13 @@ const WorkspacePane = memo(function WorkspacePane({
     paneId,
     isFocused,
     isExternalFileDropActive,
+    onPanePointerDown,
     onPaneFocus,
 }: {
     paneId: string;
     isFocused: boolean;
     isExternalFileDropActive: boolean;
+    onPanePointerDown: () => void;
     onPaneFocus: (paneId: string) => void;
 }) {
     return (
@@ -116,7 +119,10 @@ const WorkspacePane = memo(function WorkspacePane({
                       ? "inset 0 1px 0 color-mix(in srgb, var(--accent) 16%, transparent)"
                       : "none",
             }}
-            onPointerDownCapture={() => onPaneFocus(paneId)}
+            onPointerDownCapture={() => {
+                onPanePointerDown();
+                onPaneFocus(paneId);
+            }}
             onFocusCapture={() => onPaneFocus(paneId)}
             data-editor-pane-id={paneId}
             data-editor-pane-focused={isFocused || undefined}
@@ -149,6 +155,7 @@ export function WorkspaceSplitContainer({
     node,
     focusedPaneId,
     externalFileDropPaneId,
+    onPanePointerDown,
     onPaneFocus,
     onResizeSplit,
 }: WorkspaceSplitContainerProps) {
@@ -281,6 +288,7 @@ export function WorkspaceSplitContainer({
                 isExternalFileDropActive={
                     node.paneId === externalFileDropPaneId
                 }
+                onPanePointerDown={onPanePointerDown}
                 onPaneFocus={onPaneFocus}
             />
         );
@@ -320,6 +328,7 @@ export function WorkspaceSplitContainer({
                                 node={child}
                                 focusedPaneId={focusedPaneId}
                                 externalFileDropPaneId={externalFileDropPaneId}
+                                onPanePointerDown={onPanePointerDown}
                                 onPaneFocus={onPaneFocus}
                                 onResizeSplit={onResizeSplit}
                             />
diff --git a/apps/desktop/src/features/vault/FileTree.test.tsx b/apps/desktop/src/features/vault/FileTree.test.tsx
index 3b2d7a53..c4dcf811 100644
--- a/apps/desktop/src/features/vault/FileTree.test.tsx
+++ b/apps/desktop/src/features/vault/FileTree.test.tsx
@@ -20,6 +20,7 @@ import {
 import { useBookmarkStore } from "../../app/store/bookmarkStore";
 import { useSettingsStore } from "../../app/store/settingsStore";
 import { useVaultStore } from "../../app/store/vaultStore";
+import { clearFileTreeSelection } from "../../app/utils/navigation";
 import { safeStorageSetItem } from "../../app/utils/safeStorage";
 import {
     buildVaultFileEntry as buildFileEntry,
@@ -729,6 +730,154 @@ describe("FileTree", () => {
         ).toBeInTheDocument();
     });
 
+    it("clears explicit multi-selection when another pane requests it", async () => {
+        const user = userEvent.setup();
+        setVaultNotes([
+            {
+                id: "notes/alpha",
+                path: "/vault/notes/alpha.md",
+                title: "Alpha",
+                modified_at: 1,
+                created_at: 1,
+            },
+            {
+                id: "notes/beta",
+                path: "/vault/notes/beta.md",
+                title: "Beta",
+                modified_at: 1,
+                created_at: 1,
+            },
+        ]);
+
+        renderComponent(<FileTree />);
+        await expandFolder(user, "notes");
+
+        fireEvent.click(getNoteRow("Alpha"), { metaKey: true });
+        fireEvent.click(getNoteRow("Beta"), { metaKey: true });
+        expect(getNoteRow("Alpha")).toHaveAttribute("data-selected", "true");
+        expect(getNoteRow("Beta")).toHaveAttribute("data-selected", "true");
+
+        act(() => clearFileTreeSelection());
+
+        expect(getNoteRow("Alpha")).toHaveAttribute("data-selected", "false");
+        expect(getNoteRow("Beta")).toHaveAttribute("data-selected", "false");
+    });
+
+    it("clears the active tree cursor highlight when another pane requests it", async () => {
+        const user = userEvent.setup();
+        setVaultNotes([
+            {
+                id: "notes/alpha",
+                path: "/vault/notes/alpha.md",
+                title: "Alpha",
+                modified_at: 1,
+                created_at: 1,
+            },
+            {
+                id: "notes/beta",
+                path: "/vault/notes/beta.md",
+                title: "Beta",
+                modified_at: 1,
+                created_at: 1,
+            },
+        ]);
+        setEditorTabs(
+            [
+                {
+                    id: "tab-alpha",
+                    noteId: "notes/alpha",
+                    title: "Alpha",
+                    content: "Alpha",
+                },
+            ],
+            "tab-alpha",
+        );
+
+        renderComponent(<FileTree />);
+        await expandFolder(user, "notes");
+
+        await waitFor(() => {
+            expect(getNoteRow("Alpha")).toHaveAttribute(
+                "data-keyboard-focus",
+                "true",
+            );
+        });
+
+        act(() => clearFileTreeSelection());
+
+        expect(getNoteRow("Alpha")).toHaveAttribute(
+            "data-keyboard-focus",
+            "false",
+        );
+
+        await user.click(getNoteRow("Beta"));
+
+        expect(getNoteRow("Beta")).toHaveAttribute(
+            "data-keyboard-focus",
+            "true",
+        );
+    });
+
+    it("uses the active tree cursor as the shift-click range anchor", async () => {
+        const user = userEvent.setup();
+        setVaultNotes([
+            {
+                id: "notes/alpha",
+                path: "/vault/notes/alpha.md",
+                title: "Alpha",
+                modified_at: 1,
+                created_at: 1,
+            },
+            {
+                id: "notes/beta",
+                path: "/vault/notes/beta.md",
+                title: "Beta",
+                modified_at: 1,
+                created_at: 1,
+            },
+            {
+                id: "notes/gamma",
+                path: "/vault/notes/gamma.md",
+                title: "Gamma",
+                modified_at: 1,
+                created_at: 1,
+            },
+        ]);
+        setEditorTabs(
+            [
+                {
+                    id: "tab-alpha",
+                    noteId: "notes/alpha",
+                    title: "Alpha",
+                    content: "Alpha",
+                },
+            ],
+            "tab-alpha",
+        );
+
+        renderComponent(<FileTree />);
+        await expandFolder(user, "notes");
+
+        await waitFor(() => {
+            expect(getNoteRow("Alpha")).toHaveAttribute(
+                "data-keyboard-focus",
+                "true",
+            );
+        });
+
+        fireEvent.click(getNoteRow("Gamma"), { shiftKey: true });
+
+        expect(getNoteRow("Alpha")).toHaveAttribute("data-selected", "true");
+        expect(getNoteRow("Beta")).toHaveAttribute("data-selected", "true");
+        expect(getNoteRow("Gamma")).toHaveAttribute("data-selected", "true");
+
+        fireEvent.click(getNoteRow("Beta"), { shiftKey: true });
+
+        expect(getNoteRow("Alpha")).toHaveAttribute("data-selected", "true");
+        expect(getNoteRow("Beta")).toHaveAttribute("data-selected", "true");
+        expect(getNoteRow("Gamma")).toHaveAttribute("data-selected", "false");
+    });
+
     it("deletes all selected notes from the context menu", async () => {
         const user = userEvent.setup();
         const deleteNote = vi.fn().mockResolvedValue(undefined);
diff --git a/apps/desktop/src/features/vault/FileTree.tsx b/apps/desktop/src/features/vault/FileTree.tsx
index e63cc298..91b634b1 100644
--- a/apps/desktop/src/features/vault/FileTree.tsx
+++ b/apps/desktop/src/features/vault/FileTree.tsx
@@ -21,7 +21,10 @@ import {
     shouldShowVaultEntryInFileTree,
 } from "../../app/utils/vaultEntries";
 import { useSettingsStore } from "../../app/store/settingsStore";
-import { REVEAL_NOTE_IN_TREE_EVENT } from "../../app/utils/navigation";
+import {
+    CLEAR_FILE_TREE_SELECTION_EVENT,
+    REVEAL_NOTE_IN_TREE_EVENT,
+} from "../../app/utils/navigation";
 import {
     useVaultStore,
     type NoteDto,
@@ -2166,6 +2169,7 @@ export function FileTree() {
     const pendingRevealRef = useRef<string | null>(null);
     const lastClickedEntryPathRef = useRef<string | null>(null);
     const lastClickedRowKeyRef = useRef<string | null>(null);
+    const suppressActiveKeyboardCursorRef = useRef(false);
     const flatRowsRef = useRef<FlatTreeRow[]>([]);
     const displayRowsRef = useRef<FlatTreeRow[]>([]);
     const shortcutNavigableRowsRef = useRef<FlatTreeRow[]>([]);
@@ -2173,6 +2177,11 @@ export function FileTree() {
     const expandedFoldersVaultPathRef = useRef(vaultPath);
     const skipExpandedFoldersPersistRef = useRef(false);
     const restoredScrollVaultPathRef = useRef<string | null>(null);
+
+    const showTreeKeyboardCursor = useCallback((rowKey: string) => {
+        suppressActiveKeyboardCursorRef.current = false;
+        setKeyboardCursorKey(rowKey);
+    }, []);
     const suppressRevealActivePathRef = useRef<string | null>(null);
 
     // Virtualization state
@@ -2319,6 +2328,9 @@ export function FileTree() {
         );
 
         setKeyboardCursorKey((current) => {
+            if (suppressActiveKeyboardCursorRef.current) {
+                return current && visibleKeys.has(current) ? current : null;
+            }
             if (activeNoteId && visibleKeys.has(`note:${activeNoteId}`)) {
                 return `note:${activeNoteId}`;
             }
@@ -3161,7 +3173,8 @@ export function FileTree() {
 
     const selectRowRange = useCallback(
         (targetKey: string, append: boolean) => {
-            const anchorKey = lastClickedRowKeyRef.current;
+            const anchorKey =
+                lastClickedRowKeyRef.current ?? keyboardCursorKey;
             if (!anchorKey) {
                 return false;
             }
@@ -3187,9 +3200,10 @@ export function FileTree() {
             } else {
                 applySelectionState(selection);
             }
+            lastClickedRowKeyRef.current = anchorKey;
             return true;
         },
-        [applySelectionState, extendSelectionState],
+        [applySelectionState, extendSelectionState, keyboardCursorKey],
     );
 
     const handleFolderClick = useCallback(
@@ -3197,7 +3211,7 @@ export function FileTree() {
             if (wasJustDraggingRef.current) return;
             setFocusedFolderPath(path);
             const rowKey = `folder:${path}`;
-            setKeyboardCursorKey(rowKey);
+            showTreeKeyboardCursor(rowKey);
 
             if (modifiers.shift && selectRowRange(rowKey, modifiers.cmd)) {
                 return;
@@ -3220,7 +3234,7 @@ export function FileTree() {
             lastClickedRowKeyRef.current = rowKey;
             handleToggleFolder(path);
         },
-        [selectRowRange],
+        [selectRowRange, showTreeKeyboardCursor],
     );
 
     const handleRevealToggle = () => {
@@ -3353,7 +3367,7 @@ export function FileTree() {
             if (wasJustDraggingRef.current) return;
             setFocusedFolderPath(getParentPath(entry.relative_path));
             const rowKey = `entry:${entry.path}`;
-            setKeyboardCursorKey(rowKey);
+            showTreeKeyboardCursor(rowKey);
             if (modifiers.shift && selectRowRange(rowKey, modifiers.cmd)) {
                 return;
             }
@@ -3379,7 +3393,7 @@ export function FileTree() {
             lastClickedRowKeyRef.current = rowKey;
             openPdf(entry.id, entry.title, entry.path);
         },
-        [activeEntryPath, openPdf, selectRowRange],
+        [activeEntryPath, openPdf, selectRowRange, showTreeKeyboardCursor],
     );
 
     const handlePdfMouseDown = useCallback(
@@ -3472,7 +3486,7 @@ export function FileTree() {
             if (wasJustDraggingRef.current) return;
             setFocusedFolderPath(getParentPath(entry.relative_path));
             const rowKey = `entry:${entry.path}`;
-            setKeyboardCursorKey(rowKey);
+            showTreeKeyboardCursor(rowKey);
             if (modifiers.shift && selectRowRange(rowKey, modifiers.cmd)) {
                 return;
             }
@@ -3498,7 +3512,7 @@ export function FileTree() {
             lastClickedRowKeyRef.current = rowKey;
             void openVaultFileEntry(entry);
         },
-        [activeEntryPath, selectRowRange],
+        [activeEntryPath, selectRowRange, showTreeKeyboardCursor],
     );
 
     const handleFileMouseDown = useCallback(
@@ -3594,6 +3608,36 @@ export function FileTree() {
         }
     }, []);
 
+    const clearTreeSelection = useCallback(() => {
+        if (
+            selectedRowCount === 0 &&
+            lastClickedRowKeyRef.current === null &&
+            keyboardCursorKey === null
+        ) {
+            return;
+        }
+
+        suppressActiveKeyboardCursorRef.current = true;
+        setSelectedNoteIds((prev) => (prev.size === 0 ? prev : new Set()));
+        setSelectedEntryPaths((prev) => (prev.size === 0 ? prev : new Set()));
+        setSelectedFolderPaths((prev) => (prev.size === 0 ? prev : new Set()));
+        setKeyboardCursorKey(null);
+        lastClickedRowKeyRef.current = null;
+    }, [keyboardCursorKey, selectedRowCount]);
+
+    useEffect(() => {
+        window.addEventListener(
+            CLEAR_FILE_TREE_SELECTION_EVENT,
+            clearTreeSelection,
+        );
+        return () => {
+            window.removeEventListener(
+                CLEAR_FILE_TREE_SELECTION_EVENT,
+                clearTreeSelection,
+            );
+        };
+    }, [clearTreeSelection]);
+
     const clearEntrySelection = useCallback(() => {
         setSelectedEntryPaths(new Set());
         setSelectedFolderPaths(new Set());
@@ -3708,7 +3752,7 @@ export function FileTree() {
             if (wasJustDraggingRef.current) return;
             setFocusedFolderPath(getParentPath(note.id));
             const rowKey = `note:${note.id}`;
-            setKeyboardCursorKey(rowKey);
+            showTreeKeyboardCursor(rowKey);
 
             if (modifiers.shift && selectRowRange(rowKey, modifiers.cmd)) {
                 return;
@@ -3730,7 +3774,7 @@ export function FileTree() {
             lastClickedRowKeyRef.current = rowKey;
             await openTreeNote(note);
         },
-        [clearEntrySelection, openTreeNote, selectRowRange],
+        [clearEntrySelection, openTreeNote, selectRowRange, showTreeKeyboardCursor],
     );
 
     const handleNoteAuxClick = useCallback(
@@ -4373,7 +4417,7 @@ export function FileTree() {
         const rowKey = getSelectableRowKey(row);
         if (!rowKey) return;
 
-        setKeyboardCursorKey(rowKey);
+        showTreeKeyboardCursor(rowKey);
         lastClickedRowKeyRef.current = rowKey;
 
         if (row.kind === "folder") {
@@ -4398,7 +4442,7 @@ export function FileTree() {
             setSelectedFolderPaths(new Set());
             lastClickedEntryPathRef.current = row.entry.path;
         }
-    }, [clearEntrySelection]);
+    }, [clearEntrySelection, showTreeKeyboardCursor]);
 
     const activateKeyboardRow = useCallback(
         (row: FlatTreeRow) => {