diff --git a/Sources/_OpenAPIGeneratorCore/Hooks/FilteredDocument.swift b/Sources/_OpenAPIGeneratorCore/Hooks/FilteredDocument.swift
index 613aa26d..66a9b5e1 100644
--- a/Sources/_OpenAPIGeneratorCore/Hooks/FilteredDocument.swift
+++ b/Sources/_OpenAPIGeneratorCore/Hooks/FilteredDocument.swift
@@ -128,6 +128,9 @@ struct FilteredDocumentBuilder {
             }
         }
         filteredDocument.components = components
+        // Always remove webhooks, as they may contain references to schemas that were not included.
+        // Webhooks are not supported for filtering, so whenever a filter is used, all webhooks are excluded.
+        filteredDocument.webhooks = [:]
         return filteredDocument
     }
 
diff --git a/Tests/OpenAPIGeneratorCoreTests/Hooks/Test_FilteredDocument.swift b/Tests/OpenAPIGeneratorCoreTests/Hooks/Test_FilteredDocument.swift
index 5e86e060..046ed929 100644
--- a/Tests/OpenAPIGeneratorCoreTests/Hooks/Test_FilteredDocument.swift
+++ b/Tests/OpenAPIGeneratorCoreTests/Hooks/Test_FilteredDocument.swift
@@ -75,6 +75,13 @@ final class Test_FilteredDocument: XCTestCase {
                         $ref: '#/components/schemas/B'
                 Empty:
                   description: success
+            webhooks:
+              my-webhook:
+                post:
+                  description: Webhook
+                  responses:
+                    '200':
+                      description: OK
             """
         let document = try YAMLDecoder().decode(OpenAPI.Document.self, from: documentYAML)
         assert(filtering: document, filter: DocumentFilter(), hasPaths: [], hasOperations: [], hasSchemas: [])
@@ -192,5 +199,6 @@ final class Test_FilteredDocument: XCTestCase {
             file: file,
             line: line
         )
+        XCTAssertUnsortedEqual(filteredDocument.webhooks.keys, [], "Webhooks don't match", file: file, line: line)
     }
 }