diff --git a/core/deployment/src/main/java/io/quarkus/deployment/configuration/BuildTimeConfigurationReader.java b/core/deployment/src/main/java/io/quarkus/deployment/configuration/BuildTimeConfigurationReader.java
index b89cb87478bc6..645efa33e996e 100644
--- a/core/deployment/src/main/java/io/quarkus/deployment/configuration/BuildTimeConfigurationReader.java
+++ b/core/deployment/src/main/java/io/quarkus/deployment/configuration/BuildTimeConfigurationReader.java
@@ -80,6 +80,7 @@
 import io.smallrye.config.SmallRyeConfig;
 import io.smallrye.config.SmallRyeConfigBuilder;
 import io.smallrye.config.SysPropConfigSource;
+import io.smallrye.config.common.utils.StringUtil;
 
 /**
  * A configuration reader.
@@ -1017,6 +1018,9 @@ private Set<String> getAllProperties(final Set<String> registeredRoots) {
                             properties.add(property);
                         } else {
                             properties.remove(property);
+                            if (configSource instanceof EnvConfigSource) {
+                                properties.remove(StringUtil.toLowerCaseAndDotted(property));
+                            }
                         }
                     }
                 } else {