diff --git a/packages/myst-cli/src/process/mdast.ts b/packages/myst-cli/src/process/mdast.ts
index d4708c7af..d3f24f22e 100644
--- a/packages/myst-cli/src/process/mdast.ts
+++ b/packages/myst-cli/src/process/mdast.ts
@@ -172,6 +172,21 @@ export async function transformMdast(
   // This needs to come before basic transformations since it may add labels to blocks
   liftCodeMetadataToBlock(session, vfile, mdast);
 
+  // Order abbreviations by length (longest first)
+  let abbreviations: Record<string, any> | undefined;
+  if (!frontmatter.abbreviations) {
+    abbreviations = undefined;
+  } else {
+    abbreviations = Object.keys(frontmatter.abbreviations).sort().reverse().reduce(
+      (obj: Record<string, any>, key) => { 
+        const src = frontmatter.abbreviations?.[key]; 
+        obj[key] = src;
+        return obj;
+      }, 
+      {}
+    );
+  }
+  
   const pipe = unified()
     .use(reconstructHtmlPlugin) // We need to group and link the HTML first
     .use(inlineExpressionsPlugin) // Happens before math and images!
@@ -182,7 +197,7 @@ export async function transformMdast(
     .use(inlineMathSimplificationPlugin)
     .use(mathPlugin, { macros: frontmatter.math })
     .use(glossaryPlugin, { state }) // This should be before the enumerate plugins
-    .use(abbreviationPlugin, { abbreviations: frontmatter.abbreviations })
+    .use(abbreviationPlugin, { abbreviations: abbreviations })
     .use(enumerateTargetsPlugin, { state }) // This should be after math/container transforms
     .use(joinGatesPlugin);
   session.plugins?.transforms.forEach((t) => {