diff --git a/src/search.test.ts b/src/search.test.ts
index e25025f..35294e5 100644
--- a/src/search.test.ts
+++ b/src/search.test.ts
@@ -201,6 +201,7 @@ describe("createSearchController", () => {
   it("re-evaluates after reset following DOM mutation", () => {
     const c = makeContainer("<p>foo</p>");
     const ui = makeUI();
+    ui.input.value = "foo";
     const ctrl = createSearchController(c, ui);
     ctrl.setQuery("foo");
     expect(ctrl.getState().total).toBe(1);
@@ -209,6 +210,27 @@ describe("createSearchController", () => {
     expect(ctrl.getState().total).toBe(2);
   });
 
+  it("reset() drops a stale query once the field is empty (document switch)", () => {
+    // Repro of the ghost-highlight bug: user searches in doc A, empties the
+    // field, then opens doc B. loadFile() calls reset(); it must not re-apply
+    // the old query to the freshly rendered document.
+    const c = makeContainer("<p>foo foo</p>");
+    const ui = makeUI();
+    ui.input.value = "foo";
+    const ctrl = createSearchController(c, ui);
+    ctrl.setQuery("foo");
+    expect(ctrl.getState().total).toBe(2);
+
+    // User clears the field, then a new document is rendered.
+    ui.input.value = "";
+    c.innerHTML = "<p>foo bar foo</p>";
+    ctrl.reset();
+
+    expect(ctrl.getState().total).toBe(0);
+    expect(ui.counter.textContent).toBe("");
+    expect(c.querySelectorAll("mark.mdv-search-hit")).toHaveLength(0);
+  });
+
   it("recomputes when options change", () => {
     const c = makeContainer("<p>cafe café</p>");
     const ui = makeUI();
@@ -315,4 +337,33 @@ describe("createSearchController (CSS Custom Highlight API path)", () => {
     expect(reg.size).toBe(0);
     expect(ctrl.getState().total).toBe(0);
   });
+
+  it("clears highlights when a 1-char query is deleted to empty via input events", async () => {
+    vi.useFakeTimers();
+    try {
+      const { reg, createSearchController: create } =
+        await loadWithCSSHighlights();
+      const c = makeContainer("<p>eee</p>");
+      const ui = makeUI();
+      const ctrl = create(c, ui);
+
+      // Type one character; the debounced input handler applies highlights.
+      ui.input.value = "e";
+      ui.input.dispatchEvent(new Event("input"));
+      vi.advanceTimersByTime(100);
+      expect(reg.size).toBeGreaterThan(0);
+      expect(ctrl.getState().total).toBeGreaterThan(0);
+
+      // Delete it back to empty via a normal keyboard edit (input event only).
+      ui.input.value = "";
+      ui.input.dispatchEvent(new Event("input"));
+      vi.advanceTimersByTime(100);
+
+      expect(reg.size).toBe(0);
+      expect(ctrl.getState().total).toBe(0);
+      expect(ui.counter.textContent).toBe("");
+    } finally {
+      vi.useRealTimers();
+    }
+  });
 });
diff --git a/src/search.ts b/src/search.ts
index a716db0..69afbec 100644
--- a/src/search.ts
+++ b/src/search.ts
@@ -343,11 +343,24 @@ export function createSearchController(
     return index;
   }
 
+  // WebKit (WKWebView) sometimes leaves the last CSS Custom Highlight glyph
+  // painted after it is removed from the registry — most visible when the final
+  // match is deleted (query goes 1 char → 0). Nudge an imperceptible repaint of
+  // the container so the stale paint is invalidated. No-op off the CSS path.
+  function forceHighlightRepaint(): void {
+    const style = container.style;
+    const prev = style.opacity;
+    style.opacity = prev === "0.999999" ? "0.999998" : "0.999999";
+    void container.offsetHeight;
+    style.opacity = prev;
+  }
+
   function clearHighlights(): void {
     if (supportsCSSHighlights) {
       const reg = (CSS as unknown as CSSWithHighlights).highlights;
       reg.delete(HIGHLIGHT_NAME);
       reg.delete(HIGHLIGHT_CURRENT_NAME);
+      forceHighlightRepaint();
     } else {
       clearMarkFallback(container);
     }
@@ -356,6 +369,9 @@ export function createSearchController(
   function applyHighlights(): void {
     if (supportsCSSHighlights) {
       applyCSSHighlights(ranges, currentIndex);
+      if (ranges.length === 0) {
+        forceHighlightRepaint();
+      }
       return;
     }
     clearMarkFallback(container);
@@ -468,6 +484,10 @@ export function createSearchController(
     index = null;
     ranges = [];
     currentIndex = -1;
+    // Re-sync to the live input: it is the source of truth. Loading a new
+    // document must not re-highlight a stale internal query (e.g. one the user
+    // already cleared from the field) on the freshly rendered content.
+    query = ui.input.value;
     clearHighlights();
     if (query) {
       recompute();