diff --git a/.changeset/silly-taxis-suffer.md b/.changeset/silly-taxis-suffer.md
new file mode 100644
index 0000000000..7763a70f39
--- /dev/null
+++ b/.changeset/silly-taxis-suffer.md
@@ -0,0 +1,5 @@
+---
+'@backstage/repo-tools': patch
+---
+
+Fix issue where generate-patch incorrectly encodes the locator not aligning with result of yarn patch
diff --git a/packages/repo-tools/src/commands/generate-patch/generate-patch.ts b/packages/repo-tools/src/commands/generate-patch/generate-patch.ts
index 224b7ae4e6..10b31e0584 100644
--- a/packages/repo-tools/src/commands/generate-patch/generate-patch.ts
+++ b/packages/repo-tools/src/commands/generate-patch/generate-patch.ts
@@ -254,12 +254,7 @@ async function generatePatch(
   await fs.writeFile(joinPath(patchDir, name), patch, 'utf8');
 
   const locator = `${ctx.sourcePkg.packageJson.name}@npm:${version}`;
-  return `patch:${encodeURIComponent(locator)}#${posix.join(
-    '.',
-    '.yarn',
-    'patches',
-    name,
-  )}`;
+  return `patch:${locator}#${posix.join('.', '.yarn', 'patches', name)}`;
 }
 
 // Check if an existing resolution entry is a patch, and in that case return the