diff --git a/core/src/main/kotlin/plugability/DokkaContext.kt b/core/src/main/kotlin/plugability/DokkaContext.kt
index 9c9e697885..a6a3ded8cc 100644
--- a/core/src/main/kotlin/plugability/DokkaContext.kt
+++ b/core/src/main/kotlin/plugability/DokkaContext.kt
@@ -124,7 +124,7 @@ private class DokkaContextConfigurationImpl(
     }
 
     private fun findNotOverridden(bucket: Set<Extension<*, *, *>>): Extension<*, *, *> {
-        val filtered = bucket.filter { it !in suppressedExtensions }
+        val filtered = bucket.filter { it !in suppressedExtensions.filter { it.value.all { it is Suppression.ByExtension } } }
         return filtered.singleOrNull()
             ?: throw IllegalStateException("Conflicting overrides: $filtered")
     }