diff --git a/news/changelog-1.7.md b/news/changelog-1.7.md
index 62ff1c51b1..4c02248f42 100644
--- a/news/changelog-1.7.md
+++ b/news/changelog-1.7.md
@@ -28,6 +28,11 @@ All changes included in 1.7:
 ## `typst` Format
 
 - ([#11578](https://github.com/quarto-dev/quarto-cli/issues/11578)): Typst column layout widths use fractional `fr` units instead of percent `%` units for unitless and default widths in order to fill the enclosing block and not spill outside it.
+- ([#11835](https://github.com/quarto-dev/quarto-cli/issues/11835)): Take markdown structure into account when detecting minimum heading level.
+
+## `pdf` Format
+
+- ([#11835](https://github.com/quarto-dev/quarto-cli/issues/11835)): Take markdown structure into account when detecting minimum heading level.
 
 ## Lua Filters and extensions
 
diff --git a/src/core/lib/break-quarto-md.ts b/src/core/lib/break-quarto-md.ts
index 0f517ad675..dfe7ba3a02 100644
--- a/src/core/lib/break-quarto-md.ts
+++ b/src/core/lib/break-quarto-md.ts
@@ -7,7 +7,7 @@
  * Copyright (C) 2021-2022 Posit Software, PBC
  */
 
-import { lineOffsets, lines } from "./text.ts";
+import { lineOffsets } from "./text.ts";
 import { Range, rangedLines, RangedSubstring } from "./ranged-text.ts";
 import {
   asMappedString,
diff --git a/src/core/lib/markdown-analysis/level-one-headings.ts b/src/core/lib/markdown-analysis/level-one-headings.ts
new file mode 100644
index 0000000000..5722cca404
--- /dev/null
+++ b/src/core/lib/markdown-analysis/level-one-headings.ts
@@ -0,0 +1,24 @@
+/*
+ * level-one-headings.ts
+ *
+ * Copyright (C) 2025 Posit Software, PBC
+ */
+
+import { join } from "../../../deno_ral/path.ts";
+import { execProcess } from "../../process.ts";
+import { pandocBinaryPath, resourcePath } from "../../resources.ts";
+
+export async function hasLevelOneHeadings(markdown: string): Promise<boolean> {
+  // this is O(n * m) where n is the number of blocks and m is the number of matches
+  // we could do better but won't until we profile and show it's a problem
+
+  const path = pandocBinaryPath();
+  const filterPath = resourcePath(
+    join("filters", "quarto-internals", "leveloneanalysis.lua"),
+  );
+  const result = await execProcess({
+    cmd: [path, "-f", "markdown", "-t", "markdown", "-L", filterPath],
+    stdout: "piped",
+  }, markdown);
+  return result.stdout?.trim() === "true";
+}
diff --git a/src/format/pdf/format-pdf.ts b/src/format/pdf/format-pdf.ts
index eea2cbe430..cf5b1b4109 100644
--- a/src/format/pdf/format-pdf.ts
+++ b/src/format/pdf/format-pdf.ts
@@ -53,6 +53,7 @@ import { kTemplatePartials } from "../../command/render/template.ts";
 import { copyTo } from "../../core/copy.ts";
 import { kCodeAnnotations } from "../html/format-html-shared.ts";
 import { safeModeFromFile } from "../../deno_ral/fs.ts";
+import { hasLevelOneHeadings as hasL1Headings } from "../../core/lib/markdown-analysis/level-one-headings.ts";
 
 export function pdfFormat(): Format {
   return mergeConfigs(
@@ -138,7 +139,7 @@ function createPdfFormat(
       metadata: {
         ["block-headings"]: true,
       },
-      formatExtras: (
+      formatExtras: async (
         _input: string,
         markdown: string,
         flags: PandocFlags,
@@ -254,7 +255,7 @@ function createPdfFormat(
         };
 
         // Don't shift the headings if we see any H1s (we can't shift up any longer)
-        const hasLevelOneHeadings = !!markdown.match(/\n^#\s.*$/gm);
+        const hasLevelOneHeadings = await hasL1Headings(markdown);
 
         // pdfs with no other heading level oriented options get their heading level shifted by -1
         if (
diff --git a/src/format/typst/format-typst.ts b/src/format/typst/format-typst.ts
index eb2f5f4484..f36460b64b 100644
--- a/src/format/typst/format-typst.ts
+++ b/src/format/typst/format-typst.ts
@@ -29,6 +29,7 @@ import {
 } from "../../config/types.ts";
 import { formatResourcePath } from "../../core/resources.ts";
 import { createFormat } from "../formats-shared.ts";
+import { hasLevelOneHeadings as hasL1Headings } from "../../core/lib/markdown-analysis/level-one-headings.ts";
 
 export function typstFormat(): Format {
   return createFormat("Typst", "pdf", {
@@ -44,14 +45,14 @@ export function typstFormat(): Format {
       [kCiteproc]: false,
     },
     resolveFormat: typstResolveFormat,
-    formatExtras: (
+    formatExtras: async (
       _input: string,
       markdown: string,
       flags: PandocFlags,
       format: Format,
       _libDir: string,
       _services: RenderServices,
-    ): FormatExtras => {
+    ): Promise<FormatExtras> => {
       const pandoc: FormatPandoc = {};
       const metadata: Metadata = {};
 
@@ -68,7 +69,7 @@ export function typstFormat(): Format {
 
       // unless otherwise specified, pdfs with only level 2 or greater headings get their
       // heading level shifted by -1.
-      const hasLevelOneHeadings = !!markdown.match(/\n^#\s.*$/gm);
+      const hasLevelOneHeadings = await hasL1Headings(markdown);
       if (
         !hasLevelOneHeadings &&
         flags?.[kShiftHeadingLevelBy] === undefined &&
diff --git a/src/resources/filters/quarto-internals/leveloneanalysis.lua b/src/resources/filters/quarto-internals/leveloneanalysis.lua
new file mode 100644
index 0000000000..155859fc1d
--- /dev/null
+++ b/src/resources/filters/quarto-internals/leveloneanalysis.lua
@@ -0,0 +1,18 @@
+local found = false
+function Header(el)
+  found = found or el.level == 1
+  return nil
+end
+
+function Pandoc(doc)
+  if found then
+    doc.blocks = pandoc.Blocks({
+      pandoc.Str("true")
+    })
+  else
+    doc.blocks = pandoc.Blocks({
+      pandoc.Str("false")
+    })
+  end
+  return doc
+end
\ No newline at end of file
diff --git a/tests/docs/smoke-all/2025/01/10/issue-11835-b.qmd b/tests/docs/smoke-all/2025/01/10/issue-11835-b.qmd
new file mode 100644
index 0000000000..0dad5f618d
--- /dev/null
+++ b/tests/docs/smoke-all/2025/01/10/issue-11835-b.qmd
@@ -0,0 +1,17 @@
+---
+format: latex
+number-sections: true
+_quarto:
+  tests:
+    latex:
+      ensureFileRegexMatches:
+        - []
+        - ["subsection{Section}"]
+---
+
+## Section
+
+```r
+# this is a comment that shouldn't break quarto
+print("Hello, world")
+```
\ No newline at end of file
diff --git a/tests/docs/smoke-all/2025/01/10/issue-11835.qmd b/tests/docs/smoke-all/2025/01/10/issue-11835.qmd
new file mode 100644
index 0000000000..8e38c1afd8
--- /dev/null
+++ b/tests/docs/smoke-all/2025/01/10/issue-11835.qmd
@@ -0,0 +1,17 @@
+---
+format: typst
+number-sections: true
+_quarto:
+  tests:
+    typst:
+      ensurePdfRegexMatches:
+        - ["1 Section"]
+        - ["0.1 Section"]
+---
+
+## Section
+
+```r
+# this is a comment that shouldn't break quarto
+print("Hello, world")
+```
\ No newline at end of file