diff --git a/src/js/utils/flatten-annotations.ts b/src/js/utils/flatten-annotations.ts
index fa8bd931..5c69b358 100644
--- a/src/js/utils/flatten-annotations.ts
+++ b/src/js/utils/flatten-annotations.ts
@@ -33,6 +33,53 @@ function resolveStreamDict(obj: unknown): PDFDict | null {
   return null;
 }
 
+const IDENTITY_MATRIX = [1, 0, 0, 1, 0, 0];
+
+function readFormMatrix(dict: PDFDict | null): number[] {
+  if (!dict) return IDENTITY_MATRIX;
+  const matrixObj = dict.lookup(PDFName.of('Matrix'));
+  if (!(matrixObj instanceof PDFArray) || matrixObj.size() !== 6) {
+    return IDENTITY_MATRIX;
+  }
+  return extractNumbers(matrixObj, 6) ?? IDENTITY_MATRIX;
+}
+
+// ISO 32000-1 §12.5.5: map the matrix-transformed BBox onto Rect.
+// Do still applies the form Matrix, so this cm must not include it again.
+function alignAppearanceToRect(
+  bbox: number[],
+  matrix: number[],
+  x1: number,
+  y1: number,
+  x2: number,
+  y2: number
+): [number, number, number, number] | null {
+  const [a, b, c, d, e, f] = matrix;
+  let minX = Infinity;
+  let minY = Infinity;
+  let maxX = -Infinity;
+  let maxY = -Infinity;
+
+  for (const x of [bbox[0], bbox[2]]) {
+    for (const y of [bbox[1], bbox[3]]) {
+      const px = a * x + c * y + e;
+      const py = b * x + d * y + f;
+      if (px < minX) minX = px;
+      if (py < minY) minY = py;
+      if (px > maxX) maxX = px;
+      if (py > maxY) maxY = py;
+    }
+  }
+
+  const bw = maxX - minX;
+  const bh = maxY - minY;
+  if (bw < 0.001 || bh < 0.001) return null;
+
+  const sx = (x2 - x1) / bw;
+  const sy = (y2 - y1) / bh;
+  return [sx, sy, x1 - minX * sx, y1 - minY * sy];
+}
+
 export function flattenAnnotations(pdfDoc: PDFDocument): void {
   const pages = pdfDoc.getPages();
 
@@ -132,6 +179,20 @@ export function flattenAnnotations(pdfDoc: PDFDocument): void {
         }
       }
 
+      const placement = alignAppearanceToRect(
+        bbox,
+        readFormMatrix(streamDict),
+        x1,
+        y1,
+        x2,
+        y2
+      );
+      if (!placement) {
+        hasChanges = true;
+        continue;
+      }
+      const [sx, sy, tx, ty] = placement;
+
       let appRef: PDFRef;
       if (normalAppRef instanceof PDFRef) {
         appRef = normalAppRef;
@@ -140,13 +201,6 @@ export function flattenAnnotations(pdfDoc: PDFDocument): void {
       }
       const xObjKey = pageNode.newXObject('FlatAnnot', appRef);
 
-      const bw = bbox[2] - bbox[0];
-      const bh = bbox[3] - bbox[1];
-      const sx = Math.abs(bw) > 0.001 ? (x2 - x1) / bw : 1;
-      const sy = Math.abs(bh) > 0.001 ? (y2 - y1) / bh : 1;
-      const tx = x1 - bbox[0] * sx;
-      const ty = y1 - bbox[1] * sy;
-
       page.pushOperators(
         PDFOperator.of(PDFOperatorNames.PushGraphicsState),
         PDFOperator.of(PDFOperatorNames.ConcatTransformationMatrix, [
diff --git a/src/tests/flatten-annotations.test.ts b/src/tests/flatten-annotations.test.ts
index c7b2d772..a9a13ffe 100644
--- a/src/tests/flatten-annotations.test.ts
+++ b/src/tests/flatten-annotations.test.ts
@@ -1,26 +1,113 @@
 import { describe, it, expect } from 'vitest';
+import { inflateSync } from 'node:zlib';
 import {
   PDFDocument,
   PDFName,
   PDFDict,
   PDFArray,
   PDFNumber,
+  PDFRawStream,
   PDFRef,
+  PDFObject,
 } from 'pdf-lib';
 import { flattenAnnotations } from '../js/utils/flatten-annotations';
 
 function createAppearanceStream(
   doc: PDFDocument,
-  bbox: [number, number, number, number]
+  bbox: [number, number, number, number],
+  matrix?: number[] | PDFArray
 ): PDFRef {
   const stream = doc.context.stream('0 0 1 rg 0 0 100 20 re f', {
     Type: 'XObject',
     Subtype: 'Form',
     BBox: bbox,
   });
+  if (matrix) {
+    stream.dict.set(
+      PDFName.of('Matrix'),
+      Array.isArray(matrix) ? doc.context.obj(matrix) : matrix
+    );
+  }
   return doc.context.register(stream);
 }
 
+function resolve(doc: PDFDocument, ref?: PDFObject): PDFObject | undefined {
+  if (ref instanceof PDFRef) {
+    return doc.context.lookup(ref) as PDFObject | undefined;
+  }
+  return ref;
+}
+
+function decodeStream(doc: PDFDocument, ref?: PDFObject): string {
+  const stream = resolve(doc, ref);
+  if (!(stream instanceof PDFRawStream)) return '';
+  const raw = Buffer.from(stream.contents);
+  const filter = stream.dict.get(PDFName.of('Filter'));
+  return filter?.toString().includes('FlateDecode')
+    ? inflateSync(raw).toString('latin1')
+    : raw.toString('latin1');
+}
+
+function pageContent(doc: PDFDocument, pageIndex = 0): string {
+  const contents = doc.getPage(pageIndex).node.get(PDFName.of('Contents'));
+  if (!contents) return '';
+  const resolved = doc.context.lookup(contents);
+  const parts =
+    resolved instanceof PDFArray
+      ? resolved.asArray().map((entry) => decodeStream(doc, entry))
+      : [decodeStream(doc, contents)];
+  return parts.join('\n');
+}
+
+function cmBeforeDo(content: string): number[] | null {
+  const doAt = content.lastIndexOf(' Do');
+  if (doAt < 0) return null;
+  const cmAt = content.lastIndexOf(' cm', doAt);
+  if (cmAt < 0) return null;
+  const lineStart = content.lastIndexOf('\n', cmAt) + 1;
+  const operands = content.slice(lineStart, cmAt).trim().split(/\s+/);
+  if (operands.length < 6) return null;
+  const nums = operands.slice(-6).map(Number);
+  if (nums.some((n) => Number.isNaN(n))) return null;
+  return nums;
+}
+
+function expectCm(actual: number[] | null, expected: number[]) {
+  expect(actual).not.toBeNull();
+  expected.forEach((n, i) => expect(actual![i]).toBeCloseTo(n, 4));
+}
+
+function savedFormMatrix(doc: PDFDocument, pageIndex = 0): number[] | null {
+  const resources = doc.getPage(pageIndex).node.lookup(PDFName.of('Resources'));
+  if (!(resources instanceof PDFDict)) return null;
+  const xobjects = resources.lookup(PDFName.of('XObject'));
+  if (!(xobjects instanceof PDFDict)) return null;
+
+  for (const [, value] of xobjects.entries()) {
+    const obj = doc.context.lookup(value);
+    const dict =
+      obj instanceof PDFDict
+        ? obj
+        : obj !== null &&
+            typeof obj === 'object' &&
+            'dict' in obj &&
+            (obj as { dict: unknown }).dict instanceof PDFDict
+          ? (obj as { dict: PDFDict }).dict
+          : null;
+    if (!dict) continue;
+    const matrixObj = dict.lookup(PDFName.of('Matrix'));
+    if (!(matrixObj instanceof PDFArray) || matrixObj.size() !== 6) continue;
+    const nums: number[] = [];
+    for (let i = 0; i < 6; i++) {
+      const n = matrixObj.lookup(i);
+      if (!(n instanceof PDFNumber)) return null;
+      nums.push(n.asNumber());
+    }
+    return nums;
+  }
+  return null;
+}
+
 function addAnnotation(
   doc: PDFDocument,
   page: ReturnType<PDFDocument['getPage']>,
@@ -370,4 +457,116 @@ describe('flattenAnnotations', () => {
     const reloaded = await roundTrip(doc);
     expect(reloaded.getPageCount()).toBe(1);
   });
+
+  it('stamps a PDF.js FreeText appearance back onto its rectangle', async () => {
+    const doc = await PDFDocument.create();
+    const page = doc.addPage([612, 792]);
+    const rect: [number, number, number, number] = [100, 500, 250, 540];
+    const matrix = [1, 0, 0, 1, -100, -500];
+    const appRef = createAppearanceStream(doc, rect, matrix);
+
+    addAnnotation(doc, page, {
+      subtype: 'FreeText',
+      rect,
+      appearance: appRef,
+    });
+
+    flattenAnnotations(doc);
+
+    const saved = await roundTrip(doc);
+    expect(getAnnotCount(saved.getPage(0))).toBe(0);
+    expectCm(cmBeforeDo(pageContent(saved)), [1, 0, 0, 1, 100, 500]);
+    expectCm(savedFormMatrix(saved), matrix);
+  });
+
+  it('keeps an appearance with no matrix on its rectangle', async () => {
+    const doc = await PDFDocument.create();
+    const page = doc.addPage([612, 792]);
+    const appRef = createAppearanceStream(doc, [0, 0, 50, 10]);
+
+    addAnnotation(doc, page, {
+      subtype: 'FreeText',
+      rect: [80, 600, 180, 640],
+      appearance: appRef,
+    });
+
+    flattenAnnotations(doc);
+
+    const saved = await roundTrip(doc);
+    expectCm(cmBeforeDo(pageContent(saved)), [2, 0, 0, 4, 80, 600]);
+  });
+
+  it('aligns a rotated appearance box to the annotation rectangle', async () => {
+    const doc = await PDFDocument.create();
+    const page = doc.addPage([612, 792]);
+    const w = 80;
+    const h = 30;
+    const c = 0;
+    const s = 1;
+    const xs = [0, w * c, -h * s, w * c - h * s];
+    const ys = [0, w * s, h * c, w * s + h * c];
+    const matrix = [c, s, -s, c, -Math.min(...xs), -Math.min(...ys)];
+    const appRef = createAppearanceStream(doc, [0, 0, w, h], matrix);
+
+    addAnnotation(doc, page, {
+      subtype: 'FreeText',
+      rect: [40, 150, 70, 310],
+      appearance: appRef,
+    });
+
+    flattenAnnotations(doc);
+
+    const saved = await roundTrip(doc);
+    expectCm(cmBeforeDo(pageContent(saved)), [1, 0, 0, 2, 40, 150]);
+    expectCm(savedFormMatrix(saved), matrix);
+  });
+
+  it('drops an appearance whose matrix collapses the box', async () => {
+    const doc = await PDFDocument.create();
+    const page = doc.addPage([612, 792]);
+    const appRef = createAppearanceStream(
+      doc,
+      [0, 0, 100, 40],
+      [0.000004, 0, 0, 1, 0, 0]
+    );
+
+    addAnnotation(doc, page, {
+      subtype: 'FreeText',
+      rect: [10, 20, 110, 60],
+      appearance: appRef,
+    });
+
+    flattenAnnotations(doc);
+
+    const saved = await roundTrip(doc);
+    expect(getAnnotCount(saved.getPage(0))).toBe(0);
+    expect(pageContent(saved).includes(' Do')).toBe(false);
+  });
+
+  it('treats a matrix that is not six numbers as identity', async () => {
+    const doc = await PDFDocument.create();
+    const page = doc.addPage([612, 792]);
+    const other = doc.addPage([612, 792]);
+    const shortMatrix = doc.context.obj([9, 0, 0, 9, 25]) as PDFArray;
+    const namedMatrix = doc.context.obj([1, 0, 0, 1, 0, 0]) as PDFArray;
+    namedMatrix.set(4, PDFName.of('Bad'));
+
+    addAnnotation(doc, page, {
+      subtype: 'FreeText',
+      rect: [80, 600, 180, 640],
+      appearance: createAppearanceStream(doc, [0, 0, 50, 10], shortMatrix),
+    });
+    addAnnotation(doc, other, {
+      subtype: 'FreeText',
+      rect: [80, 600, 180, 640],
+      appearance: createAppearanceStream(doc, [0, 0, 50, 10], namedMatrix),
+    });
+
+    flattenAnnotations(doc);
+
+    const saved = await roundTrip(doc);
+    const expected = [2, 0, 0, 4, 80, 600];
+    expectCm(cmBeforeDo(pageContent(saved, 0)), expected);
+    expectCm(cmBeforeDo(pageContent(saved, 1)), expected);
+  });
 });