diff --git a/subprojects/dependency-management/src/integTest/groovy/org/gradle/integtests/resolve/capabilities/CapabilitiesRulesIntegrationTest.groovy b/subprojects/dependency-management/src/integTest/groovy/org/gradle/integtests/resolve/capabilities/CapabilitiesRulesIntegrationTest.groovy
index 3cf0750f5b2e..2695b10ebc49 100644
--- a/subprojects/dependency-management/src/integTest/groovy/org/gradle/integtests/resolve/capabilities/CapabilitiesRulesIntegrationTest.groovy
+++ b/subprojects/dependency-management/src/integTest/groovy/org/gradle/integtests/resolve/capabilities/CapabilitiesRulesIntegrationTest.groovy
@@ -77,6 +77,65 @@ class CapabilitiesRulesIntegrationTest extends AbstractModuleDependencyResolveTe
    Cannot select module with conflict on capability 'cglib:cglib:3.2.5' also provided by [cglib:cglib-nodep:3.2.5($variant)]""")
     }
 
+    def "implicit capability conflict is detected if implicit capability is discovered late"() {
+        given:
+        repository {
+            'cglib:cglib:3.2.5'()
+            'cglib:cglib-nodep:3.2.5'()
+            'org:lib:1.0' {
+                dependsOn 'cglib:cglib:3.2.5'
+            }
+        }
+
+        buildFile << """
+            class CapabilityRule implements ComponentMetadataRule {
+
+                @Override
+                void execute(ComponentMetadataContext context) {
+                    def details = context.details
+                    details.allVariants {
+                         withCapabilities {
+                             addCapability('cglib', 'cglib', details.id.version)
+                         }
+                     }
+                }
+            }
+
+            dependencies {
+               conf "cglib:cglib-nodep:3.2.5"
+               conf "org:lib:1.0"
+
+               components {
+                  withModule('cglib:cglib-nodep', CapabilityRule)
+               }
+            }
+        """
+
+        when:
+        repositoryInteractions {
+            'cglib:cglib-nodep:3.2.5' {
+                expectGetMetadata()
+            }
+            'cglib:cglib:3.2.5' {
+                expectGetMetadata()
+            }
+            'org:lib:1.0' {
+                expectGetMetadata()
+            }
+        }
+        fails ':checkDeps'
+
+        then:
+        def variant = 'runtime'
+        if (!isGradleMetadataPublished() && useIvy()) {
+            variant = 'default'
+        }
+        failure.assertHasCause("""Module 'cglib:cglib-nodep' has been rejected:
+   Cannot select module with conflict on capability 'cglib:cglib:3.2.5' also provided by [cglib:cglib:3.2.5($variant)]""")
+        failure.assertHasCause("""Module 'cglib:cglib' has been rejected:
+   Cannot select module with conflict on capability 'cglib:cglib:3.2.5' also provided by [cglib:cglib-nodep:3.2.5($variant)]""")
+    }
+
     @Unroll
     def "can detect conflict with capability in different versions (#rule)"() {
         given:
diff --git a/subprojects/dependency-management/src/main/java/org/gradle/api/internal/artifacts/ivyservice/resolveengine/graph/builder/DependencyGraphBuilder.java b/subprojects/dependency-management/src/main/java/org/gradle/api/internal/artifacts/ivyservice/resolveengine/graph/builder/DependencyGraphBuilder.java
index 8760f250857e..3518730a1c09 100644
--- a/subprojects/dependency-management/src/main/java/org/gradle/api/internal/artifacts/ivyservice/resolveengine/graph/builder/DependencyGraphBuilder.java
+++ b/subprojects/dependency-management/src/main/java/org/gradle/api/internal/artifacts/ivyservice/resolveengine/graph/builder/DependencyGraphBuilder.java
@@ -198,7 +198,7 @@ private void traverseGraph(final ResolveState resolveState, final Map<ModuleVers
     }
 
     private void registerCapabilities(final ResolveState resolveState, final NodeState node) {
-        node.forEachCapability(new Action<Capability>() {
+        node.forEachCapability(capabilitiesConflictHandler, new Action<Capability>() {
             @Override
             public void execute(Capability capability) {
                 // This is a performance optimization. Most modules do not declare capabilities. So, instead of systematically registering
diff --git a/subprojects/dependency-management/src/main/java/org/gradle/api/internal/artifacts/ivyservice/resolveengine/graph/builder/NodeState.java b/subprojects/dependency-management/src/main/java/org/gradle/api/internal/artifacts/ivyservice/resolveengine/graph/builder/NodeState.java
index f9206ff354a5..00858de86c5c 100644
--- a/subprojects/dependency-management/src/main/java/org/gradle/api/internal/artifacts/ivyservice/resolveengine/graph/builder/NodeState.java
+++ b/subprojects/dependency-management/src/main/java/org/gradle/api/internal/artifacts/ivyservice/resolveengine/graph/builder/NodeState.java
@@ -38,6 +38,7 @@
 import org.gradle.api.internal.artifacts.ivyservice.resolveengine.excludes.ModuleExclusions;
 import org.gradle.api.internal.artifacts.ivyservice.resolveengine.excludes.specs.ExcludeSpec;
 import org.gradle.api.internal.artifacts.ivyservice.resolveengine.graph.DependencyGraphNode;
+import org.gradle.api.internal.artifacts.ivyservice.resolveengine.graph.conflicts.CapabilitiesConflictHandler;
 import org.gradle.api.internal.artifacts.ivyservice.resolveengine.strict.StrictVersionConstraints;
 import org.gradle.api.internal.artifacts.result.DefaultResolvedVariantResult;
 import org.gradle.api.internal.attributes.ImmutableAttributes;
@@ -1037,13 +1038,16 @@ public void clearConstraintEdges(PendingDependencies pendingDependencies, NodeSt
         clearIncomingEdges();
     }
 
-    void forEachCapability(Action<? super Capability> action) {
+    void forEachCapability(CapabilitiesConflictHandler capabilitiesConflictHandler, Action<? super Capability> action) {
         List<? extends Capability> capabilities = metaData.getCapabilities().getCapabilities();
         // If there's more than one node selected for the same component, we need to add
         // the implicit capability to the list, in order to make sure we can discover conflicts
-        // between variants of the same module. Note that the fact the implicit capability is
-        // in general not included is not a bug but a performance optimization
-        if (capabilities.isEmpty() && component.hasMoreThanOneSelectedNodeUsingVariantAwareResolution()) {
+        // between variants of the same module.
+        // We also need too add the implicit capability if it was seen before as an explicit
+        // capability in order to detect the conflict between the two.
+        // Note that the fact that the implicit capability is not included in other cases
+        // is not a bug but a performance optimization.
+        if (capabilities.isEmpty() && (component.hasMoreThanOneSelectedNodeUsingVariantAwareResolution() || capabilitiesConflictHandler.hasSeenCapability(component.getImplicitCapability()))) {
             action.execute(component.getImplicitCapability());
         } else {
             // The isEmpty check is not required, might look innocent, but Guava's performance bad for an empty immutable list
diff --git a/subprojects/dependency-management/src/main/java/org/gradle/api/internal/artifacts/ivyservice/resolveengine/graph/conflicts/CapabilitiesConflictHandler.java b/subprojects/dependency-management/src/main/java/org/gradle/api/internal/artifacts/ivyservice/resolveengine/graph/conflicts/CapabilitiesConflictHandler.java
index 4660df0dadb5..ccdaa9927a87 100644
--- a/subprojects/dependency-management/src/main/java/org/gradle/api/internal/artifacts/ivyservice/resolveengine/graph/conflicts/CapabilitiesConflictHandler.java
+++ b/subprojects/dependency-management/src/main/java/org/gradle/api/internal/artifacts/ivyservice/resolveengine/graph/conflicts/CapabilitiesConflictHandler.java
@@ -23,6 +23,13 @@
 import java.util.Collection;
 
 public interface CapabilitiesConflictHandler extends ConflictHandler<CapabilitiesConflictHandler.Candidate, ConflictResolutionResult, CapabilitiesConflictHandler.Resolver> {
+
+    /**
+     * Was the given capability already seen which might require a conflict check later?
+     * This is needed to determine if also implicit capabilities need to enter conflict detection.
+     */
+    boolean hasSeenCapability(Capability capability);
+
     interface Candidate {
         NodeState getNode();
         Capability getCapability();
diff --git a/subprojects/dependency-management/src/main/java/org/gradle/api/internal/artifacts/ivyservice/resolveengine/graph/conflicts/DefaultCapabilitiesConflictHandler.java b/subprojects/dependency-management/src/main/java/org/gradle/api/internal/artifacts/ivyservice/resolveengine/graph/conflicts/DefaultCapabilitiesConflictHandler.java
index 802a7c103784..ee824269266f 100644
--- a/subprojects/dependency-management/src/main/java/org/gradle/api/internal/artifacts/ivyservice/resolveengine/graph/conflicts/DefaultCapabilitiesConflictHandler.java
+++ b/subprojects/dependency-management/src/main/java/org/gradle/api/internal/artifacts/ivyservice/resolveengine/graph/conflicts/DefaultCapabilitiesConflictHandler.java
@@ -139,6 +139,11 @@ public void registerResolver(Resolver conflictResolver) {
         resolvers.add(conflictResolver);
     }
 
+    @Override
+    public boolean hasSeenCapability(Capability capability) {
+        return capabilityWithoutVersionToNodes.containsKey(((CapabilityInternal) capability).getCapabilityId());
+    }
+
     public static CapabilitiesConflictHandler.Candidate candidate(NodeState node, Capability capability, Collection<NodeState> implicitCapabilityProviders) {
         return new Candidate(node, capability, implicitCapabilityProviders);
     }