diff --git a/.changeset/repo-tools-boo-descriptions-two-electric-boogaloo.md b/.changeset/repo-tools-boo-descriptions-two-electric-boogaloo.md
new file mode 100644
index 0000000000..8cb6d49153
--- /dev/null
+++ b/.changeset/repo-tools-boo-descriptions-two-electric-boogaloo.md
@@ -0,0 +1,5 @@
+---
+'@backstage/repo-tools': patch
+---
+
+Fixed a bug with the `generate-catalog-info` command that could cause `metadata.description` values to be overwritten by `package.json` description values only because unrelated attributes were being changed.
diff --git a/packages/repo-tools/src/commands/generate-catalog-info/generate-catalog-info.ts b/packages/repo-tools/src/commands/generate-catalog-info/generate-catalog-info.ts
index 38bc3ab4b2..b8a473c67b 100644
--- a/packages/repo-tools/src/commands/generate-catalog-info/generate-catalog-info.ts
+++ b/packages/repo-tools/src/commands/generate-catalog-info/generate-catalog-info.ts
@@ -253,7 +253,7 @@ function createOrMergeEntity(
       // Provide default name/title/description values.
       name: safeEntityName,
       title: packageJson.name,
-      ...(packageJson.description
+      ...(packageJson.description && !existingEntity.metadata?.description
         ? { description: packageJson.description }
         : undefined),
     },