diff --git a/lib/workers/repository/init/config.js b/lib/workers/repository/init/config.js
index a2313a0baff7885401828d98a20a3f697e809c6f..5205bb86444115927f5c123dbb69e7efefbf8fc5 100644
--- a/lib/workers/repository/init/config.js
+++ b/lib/workers/repository/init/config.js
@@ -22,12 +22,6 @@ async function mergeRenovateConfig(config) {
     logger.debug({ renovateJson }, 'mirrorMode config');
     const migratedConfig = await migrateAndValidate(config, renovateJson);
     const resolvedConfig = await presets.resolveConfigPresets(migratedConfig);
-    if (resolvedConfig.npmrc) {
-      logger.debug(
-        'Ignoring any .npmrc files in repository due to configured npmrc'
-      );
-      resolvedConfig.ignoreNpmrcFile = true;
-    }
     returnConfig = mergeChildConfig(returnConfig, resolvedConfig);
     returnConfig.renovateJsonPresent = true;
     return returnConfig;
@@ -139,6 +133,13 @@ async function mergeRenovateConfig(config) {
   );
   delete resolvedConfig.privateKey;
   logger.trace({ config: resolvedConfig }, 'resolved config');
+  // istanbul ignore if
+  if (resolvedConfig.npmrc) {
+    logger.debug(
+      'Ignoring any .npmrc files in repository due to configured npmrc'
+    );
+    resolvedConfig.ignoreNpmrcFile = true;
+  }
   returnConfig = mergeChildConfig(returnConfig, resolvedConfig);
   returnConfig.renovateJsonPresent = true;
   returnConfig.packageRules = flattenPackageRules(returnConfig.packageRules);