diff --git a/core/deployment/src/main/java/io/quarkus/deployment/configuration/RunTimeConfigurationGenerator.java b/core/deployment/src/main/java/io/quarkus/deployment/configuration/RunTimeConfigurationGenerator.java
index d561e386b5b9d..9136c61a379c7 100644
--- a/core/deployment/src/main/java/io/quarkus/deployment/configuration/RunTimeConfigurationGenerator.java
+++ b/core/deployment/src/main/java/io/quarkus/deployment/configuration/RunTimeConfigurationGenerator.java
@@ -453,6 +453,9 @@ public void run() {
             final ConfigPatternMap<Container> runTimeIgnored = ConfigPatternMap
                     .merge(ConfigPatternMap.merge(buildTimePatternMap,
                             buildTimeRunTimePatternMap, combinator), bootstrapPatternMap, combinator);
+            final ConfigPatternMap<Container> bootstrapIgnored = ConfigPatternMap
+                    .merge(ConfigPatternMap.merge(buildTimePatternMap,
+                            buildTimeRunTimePatternMap, combinator), runTimePatternMap, combinator);
 
             final MethodDescriptor siParserBody = generateParserBody(buildTimeRunTimePatternMap, buildTimeRunTimeIgnored,
                     new StringBuilder("siParseKey"), false, Type.BUILD_TIME);
@@ -460,7 +463,7 @@ public void run() {
                     new StringBuilder("rtParseKey"), false, Type.RUNTIME);
             MethodDescriptor bsParserBody = null;
             if (bootstrapConfigSetupNeeded()) {
-                bsParserBody = generateParserBody(bootstrapPatternMap, null,
+                bsParserBody = generateParserBody(bootstrapPatternMap, bootstrapIgnored,
                         new StringBuilder("bsParseKey"), false, Type.BOOTSTRAP);
             }