diff --git a/news/changelog-1.8.md b/news/changelog-1.8.md
index 0bc7f25cd00..5061c1489de 100644
--- a/news/changelog-1.8.md
+++ b/news/changelog-1.8.md
@@ -60,4 +60,5 @@ All changes included in 1.8:
 
 ## Other fixes and improvements
 
+- ([#11321](https://github.com/quarto-dev/quarto-cli/issues/11321)): Follow [recommendation from LaTeX project](https://latex-project.org/news/latex2e-news/ltnews40.pdf) and use `lualatex` instead of `xelatex` as the default PDF engine.
 - ([#12782](https://github.com/quarto-dev/quarto-cli/pull/12782)): fix bug on `safeRemoveDirSync`'s detection of safe directory boundaries.
\ No newline at end of file
diff --git a/src/command/render/render-contexts.ts b/src/command/render/render-contexts.ts
index b02c2df565d..8b020f27180 100644
--- a/src/command/render/render-contexts.ts
+++ b/src/command/render/render-contexts.ts
@@ -505,39 +505,6 @@ async function resolveFormats(
     const directoryFormat = directoryFormats[format].format;
     const inputFormat = inputFormats[format].format;
 
-    // resolve theme (project-level bootstrap theme always wins for web drived output)
-    if (
-      project &&
-      (isHtmlOutput(format, true) || isHtmlDashboardOutput(format)) &&
-      formatHasBootstrap(projFormat) && projectTypeIsWebsite(projType)
-    ) {
-      // if (formatHasBootstrap(inputFormat)) {
-      //   if (
-      //     inputFormat.metadata[kTheme] !== undefined &&
-      //     !ld.isEqual(inputFormat.metadata[kTheme], projFormat.metadata[kTheme])
-      //   ) {
-      //     warnOnce(
-      //       `The file ${file.path} contains a theme property which is being ignored. Website projects do not support per document themes since all pages within a website share the website's theme.`,
-      //     );
-      //   }
-      //   delete inputFormat.metadata[kTheme];
-      // }
-      // if (formatHasBootstrap(directoryFormat)) {
-      //   if (
-      //     directoryFormat.metadata[kTheme] !== undefined &&
-      //     !ld.isEqual(
-      //       directoryFormat.metadata[kTheme],
-      //       projFormat.metadata[kTheme],
-      //     )
-      //   ) {
-      //     warnOnce(
-      //       `The file ${file.path} contains a theme provided by a metadata file. This theme metadata is being ignored. Website projects do not support per directory themes since all pages within a website share the website's theme.`,
-      //     );
-      //   }
-      //   delete directoryFormat.metadata[kTheme];
-      // }
-    }
-
     // combine user formats
     const userFormat = mergeFormatMetadata(
       projFormat || {},
diff --git a/src/format/pdf/format-pdf.ts b/src/format/pdf/format-pdf.ts
index 32f3d999ef1..4e80f00d559 100644
--- a/src/format/pdf/format-pdf.ts
+++ b/src/format/pdf/format-pdf.ts
@@ -128,7 +128,7 @@ function createPdfFormat(
         [kFigDpi]: 300,
       },
       pandoc: {
-        [kPdfEngine]: "xelatex",
+        [kPdfEngine]: "lualatex",
         standalone: true,
         variables: {
           graphics: true,