diff --git a/extensions/vscode/src/inspect/detectors/quarto.test.ts b/extensions/vscode/src/inspect/detectors/quarto.test.ts
index f1de85b9f..ae3867466 100644
--- a/extensions/vscode/src/inspect/detectors/quarto.test.ts
+++ b/extensions/vscode/src/inspect/detectors/quarto.test.ts
@@ -348,6 +348,46 @@ describe("QuartoDetector", () => {
     expect(configs[0]?.files).toContain("/doc.qmd");
   });
 
+  test("fallback when quarto binary missing: .qmd with R chunks detects knitr engine (#3993)", async () => {
+    setupGlobDir(["report.qmd"]);
+    mockAccess.mockRejectedValue(new Error("ENOENT"));
+    mockReadFile.mockResolvedValue(
+      '---\ntitle: "Report"\n---\n\n```{r}\nsource("helpers.R")\n```\n',
+    );
+
+    // quarto inspect fails (not installed)
+    mockExecFile.mockRejectedValue(
+      Object.assign(new Error("spawn quarto ENOENT"), { code: "ENOENT" }),
+    );
+
+    const configs = await detector.inferType("/project", "report.qmd");
+    expect(configs).toHaveLength(1);
+    expect(configs[0]?.type).toBe(ContentType.QUARTO_STATIC);
+    expect(configs[0]?.r).toEqual({});
+    expect(configs[0]?.quarto).toEqual({
+      version: "1.7.34",
+      engines: ["knitr"],
+    });
+  });
+
+  test("fallback when quarto binary missing: .qmd with Python chunks detects jupyter engine", async () => {
+    setupGlobDir(["analysis.qmd"]);
+    mockAccess.mockRejectedValue(new Error("ENOENT"));
+    mockReadFile.mockResolvedValue("```{python}\nimport pandas as pd\n```\n");
+
+    mockExecFile.mockRejectedValue(
+      Object.assign(new Error("spawn quarto ENOENT"), { code: "ENOENT" }),
+    );
+
+    const configs = await detector.inferType("/project", "analysis.qmd");
+    expect(configs).toHaveLength(1);
+    expect(configs[0]?.python).toEqual({});
+    expect(configs[0]?.quarto).toEqual({
+      version: "1.7.34",
+      engines: ["jupyter"],
+    });
+  });
+
   test("fallback when quarto binary missing: .ipynb", async () => {
     setupGlobDir(["notebook.ipynb"]);
     mockAccess.mockRejectedValue(new Error("ENOENT"));
@@ -386,6 +426,27 @@ describe("QuartoDetector", () => {
     });
   });
 
+  test("directory inspection with empty engines falls back to file scanning (#3993)", async () => {
+    setupGlobDir([]);
+    mockAccess.mockRejectedValue(new Error("ENOENT"));
+    mockReadFile.mockResolvedValue('```{r}\nsource("script.R")\n```\n');
+
+    // quarto inspect returns empty engines (simulating older quarto or edge case)
+    const inspectJson = makeInspectOutput({
+      engines: [],
+      files: { input: ["/project/report.qmd"], configResources: [] },
+      formats: {
+        html: { metadata: { title: "Report" }, pandoc: {} },
+      },
+    });
+    mockExecFile.mockResolvedValue({ stdout: inspectJson });
+
+    const configs = await detector.inferType("/project", "_quarto.yml");
+    expect(configs).toHaveLength(1);
+    expect(configs[0]?.r).toEqual({});
+    expect(configs[0]?.quarto?.engines).toContain("knitr");
+  });
+
   test("skips non-quarto entrypoints", async () => {
     const configs = await detector.inferType("/project", "index.html");
     expect(configs).toHaveLength(0);
diff --git a/extensions/vscode/src/inspect/detectors/quarto.ts b/extensions/vscode/src/inspect/detectors/quarto.ts
index f69f7791a..32a4690e8 100644
--- a/extensions/vscode/src/inspect/detectors/quarto.ts
+++ b/extensions/vscode/src/inspect/detectors/quarto.ts
@@ -180,6 +180,28 @@ export class QuartoDetector implements ContentTypeDetector {
           );
         }
       }
+    } else if (inspectOutput.engines.length === 0) {
+      // Directory inspection returned no engines — scan input files to detect
+      // languages so we can populate engines as a fallback.
+      for (const inputFile of inspectOutput.inputFiles()) {
+        if (needR && needPython) break;
+        const abs = path.isAbsolute(inputFile)
+          ? inputFile
+          : path.join(baseDir, inputFile);
+        const ext = path.extname(abs).toLowerCase();
+        if (ext === ".ipynb") {
+          needPython = true;
+        } else if (quartoSuffixesLower.includes(ext)) {
+          try {
+            const content = await fs.readFile(abs, "utf-8");
+            const langs = detectMarkdownLanguagesInContent(content);
+            needR = needR || langs.needsR;
+            needPython = needPython || langs.needsPython;
+          } catch {
+            // Cannot read file — skip
+          }
+        }
+      }
     }
 
     const engines = [...inspectOutput.engines];
@@ -508,11 +530,41 @@ export class QuartoDetector implements ContentTypeDetector {
       return cfg;
     }
 
-    // Include .qmd files
+    // Include .qmd files and detect languages from their content
     const qmdFiles = await globDir(baseDir, "*.qmd");
+    let needR = false;
+    let needPython = false;
+
     for (const qmdPath of qmdFiles) {
       const relPath = path.basename(qmdPath);
       files.push(`/${relPath}`);
+
+      // Detect language needs from file content
+      if (!needR || !needPython) {
+        try {
+          const content = await fs.readFile(qmdPath, "utf-8");
+          const langs = detectMarkdownLanguagesInContent(content);
+          needR = needR || langs.needsR;
+          needPython = needPython || langs.needsPython;
+        } catch {
+          // Cannot read file — skip language detection for this file
+        }
+      }
+    }
+
+    // Set engines based on detected languages
+    const engines: string[] = [];
+    if (needR) {
+      cfg.r = {};
+      engines.push("knitr");
+    }
+    if (needPython) {
+      cfg.python = {};
+      engines.push("jupyter");
+    }
+    if (engines.length > 0) {
+      engines.sort();
+      cfg.quarto = { version: defaultQuartoVersion, engines };
     }
 
     // Include special yml files