diff --git a/lib/workers/repository/updates/flatten.js b/lib/workers/repository/updates/flatten.js
index 85a6488f2f5cf90daa40bd001c2b26868ab07ea5..2caf46351553e28f8f9bb78dcac0fee220be84ef 100644
--- a/lib/workers/repository/updates/flatten.js
+++ b/lib/workers/repository/updates/flatten.js
@@ -24,11 +24,14 @@ function flattenUpdates(config, packageFiles) {
             let updateConfig = mergeChildConfig(depConfig, update);
             delete updateConfig.updates;
             updateConfig = applyPackageRules(updateConfig);
+            // Now we're finished with these packageRules
+            updateConfig.packageRules = [];
             // apply major/minor/patch/pin/digest
             updateConfig = mergeChildConfig(
               updateConfig,
               updateConfig[updateConfig.updateType]
             );
+            // Apply again in case any were added by the updateType config
             updateConfig = applyPackageRules(updateConfig);
             updateConfig.depNameSanitized = updateConfig.depName
               ? updateConfig.depName