diff --git a/.changeset/config-reader-registry-sync-npmrc.md b/.changeset/config-reader-registry-sync-npmrc.md
new file mode 100644
index 0000000000..4ce0d1cf77
--- /dev/null
+++ b/.changeset/config-reader-registry-sync-npmrc.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/config.reader": patch
+"pnpm": patch
+---
+
+Fix `config.registry` getting a trailing slash appended when `registry` is set in `.npmrc` and no `registries.default` is provided by `pnpm-workspace.yaml`. The sync from `registries.default` to `config.registry` introduced in #11744 now only fires when the workspace manifest actually contributes a different default.
diff --git a/config/reader/src/index.ts b/config/reader/src/index.ts
index 6083ebe906..2bc79a6627 100644
--- a/config/reader/src/index.ts
+++ b/config/reader/src/index.ts
@@ -463,9 +463,10 @@ export async function getConfig (opts: {
 
   // Sync registries.default to the top-level registry property so that
   // commands like login/logout that use opts.registry pick up the default
-  // registry configured in pnpm-workspace.yaml.
-  // Only sync when registry was not explicitly set via CLI.
-  if (!explicitlySetKeys.has('registry')) {
+  // registry configured in pnpm-workspace.yaml. Only sync when the workspace
+  // manifest actually contributed a different default than what .npmrc provided,
+  // and when registry was not explicitly set via CLI.
+  if (!explicitlySetKeys.has('registry') && pnpmConfig.registries.default !== registriesFromNpmrc.default) {
     pnpmConfig.registry = pnpmConfig.registries.default
   }