diff --git a/news/changelog-1.7.md b/news/changelog-1.7.md
index 9a0f4f8bc6..3d21616046 100644
--- a/news/changelog-1.7.md
+++ b/news/changelog-1.7.md
@@ -108,6 +108,10 @@ All changes included in 1.7:
 - ([#11664](https://github.com/quarto-dev/quarto-cli/issues/11664)): `lipsum` shortcode is no longer randomly generated by default, use `{{< lipsum random=true >}}` to restore randomness.
 - ([#11379](https://github.com/quarto-dev/quarto-cli/issues/11379)): Add `version` shortcode to display the current Quarto version.
 
+## Quarto Lua API
+
+- ([#12299](https://github.com/quarto-dev/quarto-cli/issues/12299)): `quarto.doc.pdf_engine()` now correctly returns the PDF engine used for the document. `quarto.doc.cite_method()` now returns `nil` if no citation method will be used (i.e. no references is the document set).
+
 ## Engines
 
 ### `julia`
diff --git a/src/command/render/filters.ts b/src/command/render/filters.ts
index 20fd5e9764..bae4f4d1a1 100644
--- a/src/command/render/filters.ts
+++ b/src/command/render/filters.ts
@@ -838,7 +838,7 @@ function citeMethod(options: PandocOptions): CiteMethod | null {
 
 function pdfEngine(options: PandocOptions): string {
   const pdfEngine = options.flags?.pdfEngine ||
-    options.metadata?.[kPdfEngine] as string ||
+    options.format.pandoc?.[kPdfEngine] as string ||
     "pdflatex";
   return pdfEngine;
 }
diff --git a/src/resources/pandoc/datadir/init.lua b/src/resources/pandoc/datadir/init.lua
index 26317928b6..0835e7d031 100644
--- a/src/resources/pandoc/datadir/init.lua
+++ b/src/resources/pandoc/datadir/init.lua
@@ -2082,7 +2082,7 @@ quarto = {
     is_format = format.isFormat,
 
     cite_method = function() 
-      local citeMethod = param('cite-method', 'citeproc')
+      local citeMethod = param('cite-method', nil)
       return citeMethod
     end,
     pdf_engine = function() 
diff --git a/tests/docs/smoke-all/2025/03/27/12299-1.lua b/tests/docs/smoke-all/2025/03/27/12299-1.lua
new file mode 100644
index 0000000000..3c9cb9071d
--- /dev/null
+++ b/tests/docs/smoke-all/2025/03/27/12299-1.lua
@@ -0,0 +1,5 @@
+function Pandoc(doc)
+  assert(quarto.doc.pdf_engine() == "xelatex", "`quarto.doc.pdf_engine()` should be xelatex but is instead: " .. quarto.doc.pdf_engine())
+  assert(quarto.doc.cite_method() == "natbib", "`quarto.doc.cite_method()` should return natbib but return instead: " .. (quarto.doc.cite_method() or 'unset'))
+  return doc
+end
\ No newline at end of file
diff --git a/tests/docs/smoke-all/2025/03/27/12299-1.qmd b/tests/docs/smoke-all/2025/03/27/12299-1.qmd
new file mode 100644
index 0000000000..47857e4ff6
--- /dev/null
+++ b/tests/docs/smoke-all/2025/03/27/12299-1.qmd
@@ -0,0 +1,34 @@
+---
+title: testing Lua API value for latex
+format:
+  latex:
+    pdf-engine: xelatex
+    cite-method: natbib
+references:
+- type: article-journal
+  id: WatsonCrick1953
+  author:
+  - family: Watson
+    given: J. D.
+  - family: Crick
+    given: F. H. C.
+  issued:
+    date-parts:
+    - - 1953
+      - 4
+      - 25
+  title: 'Molecular structure of nucleic acids: a structure for
+    deoxyribose nucleic acid'
+  title-short: Molecular structure of nucleic acids
+  container-title: Nature
+  volume: 171
+  issue: 4356
+  page: 737-738
+  DOI: 10.1038/171737a0
+  URL: https://www.nature.com/articles/171737a0
+  language: en-GB
+filters:
+  - 12299-1.lua
+---
+
+
diff --git a/tests/docs/smoke-all/2025/03/27/12299.lua b/tests/docs/smoke-all/2025/03/27/12299.lua
new file mode 100644
index 0000000000..d309fc1746
--- /dev/null
+++ b/tests/docs/smoke-all/2025/03/27/12299.lua
@@ -0,0 +1,5 @@
+function Pandoc(doc)
+  assert(quarto.doc.pdf_engine() == "xelatex", "`quarto.doc.pdf_engine()` should be xelatex but is instead: " .. quarto.doc.pdf_engine())
+  assert(quarto.doc.cite_method() == nil, "`quarto.doc.cite_method()` should return natbib but return instead: " .. (quarto.doc.cite_method() or 'unset'))
+  return doc
+end
\ No newline at end of file
diff --git a/tests/docs/smoke-all/2025/03/27/12299.qmd b/tests/docs/smoke-all/2025/03/27/12299.qmd
new file mode 100644
index 0000000000..11238be328
--- /dev/null
+++ b/tests/docs/smoke-all/2025/03/27/12299.qmd
@@ -0,0 +1,11 @@
+---
+title: testing Lua API value for latex
+format:
+  latex:
+    pdf-engine: xelatex
+    cite-method: natbib
+filters:
+  - 12299.lua
+---
+
+