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 a14c1d0c61470..ea46e31c3a26a 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
@@ -227,6 +227,9 @@ public final class RunTimeConfigurationGenerator {
 
     static final MethodDescriptor PU_IS_PROPERTY_IN_ROOT = MethodDescriptor.ofMethod(PropertiesUtil.class,
             "isPropertyInRoot", boolean.class, Set.class, NameIterator.class);
+    static final MethodDescriptor PU_FILTER_PROPERTIES_IN_ROOTS = MethodDescriptor.ofMethod(PropertiesUtil.class,
+            "filterPropertiesInRoots", Iterable.class, Iterable.class, Set.class);
+
     static final MethodDescriptor PU_IS_PROPERTY_QUARKUS_COMPOUND_NAME = MethodDescriptor.ofMethod(PropertiesUtil.class,
             "isPropertyQuarkusCompoundName", boolean.class, NameIterator.class);
     static final MethodDescriptor PU_FILTER_UNKNOWN = MethodDescriptor.ofMethod(PropertiesUtil.class, "filterUnknown",
@@ -668,16 +671,10 @@ public void run() {
 
         private void configSweepLoop(MethodDescriptor parserBody, MethodCreator method, ResultHandle config,
                 Set<String> registeredRoots, Type type) {
-            ResultHandle rootSet;
             ResultHandle nameSet;
             ResultHandle iterator;
 
-            rootSet = method.newInstance(HS_NEW);
-            for (String registeredRoot : registeredRoots) {
-                method.invokeVirtualMethod(HS_ADD, rootSet, method.load(registeredRoot));
-            }
-
-            nameSet = method.invokeVirtualMethod(SRC_GET_PROPERTY_NAMES, config);
+            nameSet = filterProperties(method, config, registeredRoots);
             iterator = method.invokeInterfaceMethod(ITRA_ITERATOR, nameSet);
 
             try (BytecodeCreator sweepLoop = method.createScope()) {
@@ -701,8 +698,6 @@ private void configSweepLoop(MethodDescriptor parserBody, MethodCreator method,
                     // if (! keyIter.hasNext()) continue sweepLoop;
                     hasNext.ifNonZero(hasNext.invokeVirtualMethod(NI_HAS_NEXT, keyIter)).falseBranch().continueScope(sweepLoop);
                     // if (! keyIter.nextSegmentEquals("quarkus")) continue sweepLoop;
-                    hasNext.ifNonZero(hasNext.invokeStaticMethod(PU_IS_PROPERTY_IN_ROOT, rootSet, keyIter)).falseBranch()
-                            .continueScope(sweepLoop);
                     // parse(config, keyIter);
                     hasNext.invokeStaticMethod(parserBody, config, keyIter);
                     // continue sweepLoop;
@@ -711,6 +706,21 @@ private void configSweepLoop(MethodDescriptor parserBody, MethodCreator method,
             }
         }
 
+        private ResultHandle filterProperties(MethodCreator method, ResultHandle config, Set<String> registeredRoots) {
+            // Roots
+            ResultHandle rootSet;
+            rootSet = method.newInstance(HS_NEW);
+            for (String registeredRoot : registeredRoots) {
+                method.invokeVirtualMethod(HS_ADD, rootSet, method.load(registeredRoot));
+            }
+
+            // PropertyNames
+            ResultHandle properties = method.invokeVirtualMethod(SRC_GET_PROPERTY_NAMES, config);
+
+            // Filtered Properties
+            return method.invokeStaticMethod(PU_FILTER_PROPERTIES_IN_ROOTS, properties, rootSet);
+        }
+
         private Set<String> getRegisteredRoots(ConfigPhase configPhase) {
             Set<String> registeredRoots = new HashSet<>();
             for (RootDefinition root : roots) {
diff --git a/core/runtime/src/main/java/io/quarkus/runtime/configuration/PropertiesUtil.java b/core/runtime/src/main/java/io/quarkus/runtime/configuration/PropertiesUtil.java
index a1683b240edf4..4a87c6b0f191a 100644
--- a/core/runtime/src/main/java/io/quarkus/runtime/configuration/PropertiesUtil.java
+++ b/core/runtime/src/main/java/io/quarkus/runtime/configuration/PropertiesUtil.java
@@ -1,6 +1,8 @@
 package io.quarkus.runtime.configuration;
 
+import java.util.ArrayList;
 import java.util.HashSet;
+import java.util.List;
 import java.util.Set;
 
 import io.smallrye.config.KeyMap;
@@ -51,11 +53,55 @@ public static boolean isPropertyInRoot(Set<String> roots, NameIterator propertyN
         return false;
     }
 
-    public static boolean isPropertyQuarkusCompoundName(NameIterator propertyName) {
-        if (propertyName.hasNext()) {
-            return propertyName.getNextSegment().startsWith("quarkus.");
+    public static Iterable<String> filterPropertiesInRoots(final Iterable<String> properties, final Set<String> roots) {
+        if (roots.isEmpty()) {
+            return properties;
         }
-        return false;
+
+        // Will match everything, so no point in filtering
+        if (roots.contains("")) {
+            return properties;
+        }
+
+        List<String> matchedProperties = new ArrayList<>();
+        for (String property : properties) {
+            // This is a Quarkus compound name, usually by setting something like `quarkus.foo.bar` in the YAML source
+            // TODO - We let it through to match it later again to place it in the right unknown reporting (static or runtime). We can improve this too.
+            if (property.startsWith("\"quarkus.")) {
+                matchedProperties.add(property);
+                continue;
+            }
+
+            for (String root : roots) {
+                // if property is less than the root no way to match
+                if (property.length() < root.length()) {
+                    continue;
+                }
+
+                // if it is the same, then it can still map with parent name
+                if (property.equals(root)) {
+                    matchedProperties.add(property);
+                    break;
+                } else if (property.length() == root.length()) {
+                    continue;
+                }
+
+                // foo.bar
+                // foo.bar."baz"
+                // foo.bar[0]
+                char c = property.charAt(root.length());
+                if ((c == '.') || c == '[') {
+                    if (property.startsWith(root)) {
+                        matchedProperties.add(property);
+                    }
+                }
+            }
+        }
+        return matchedProperties;
+    }
+
+    public static boolean isPropertyQuarkusCompoundName(NameIterator propertyName) {
+        return propertyName.getName().startsWith("\"quarkus.");
     }
 
     /**