diff --git a/javascript/ql/lib/change-notes/2026-09-10-fastify-chainable-config-methods.md b/javascript/ql/lib/change-notes/2026-09-10-fastify-chainable-config-methods.md
new file mode 100644
index 000000000000..986788d62111
--- /dev/null
+++ b/javascript/ql/lib/change-notes/2026-09-10-fastify-chainable-config-methods.md
@@ -0,0 +1,4 @@
+---
+category: minorAnalysis
+---
+* Fastify servers reached through a chainable configuration method, such as `fastify().withTypeProvider<T>()` or `fastify().setValidatorCompiler(...)`, are now recognized as the same server instance. Routes registered on such an instance are now attributed to their server, which may add results for queries such as `js/missing-rate-limiting` where routes were previously not recognized at all, and remove false positives where a globally registered plugin guards them.
diff --git a/javascript/ql/lib/semmle/javascript/frameworks/Fastify.qll b/javascript/ql/lib/semmle/javascript/frameworks/Fastify.qll
index 26dde3fc78bd..63b6072d8ffa 100644
--- a/javascript/ql/lib/semmle/javascript/frameworks/Fastify.qll
+++ b/javascript/ql/lib/semmle/javascript/frameworks/Fastify.qll
@@ -21,6 +21,27 @@ module Fastify {
     StandardServerDefinition() { this = DataFlow::moduleImport("fastify").getAnInvocation() }
   }
 
+  /**
+   * Gets the name of a chainable Fastify configuration method, that is, a method that
+   * configures the server instance and returns that same instance, so that a call to it
+   * still refers to the server.
+   *
+   * Plugin, hook and route registration (`register`, `addHook`, `onClose`, and the
+   * shorthand route methods) returns the server as well, but is deliberately excluded
+   * here, because it already has a meaning in the routing model for Fastify. The
+   * lifecycle methods `after` and `ready` are excluded too: `after` returns the server
+   * only when it is given a callback, and `ready` never does.
+   */
+  private string chainableConfigMethodName() {
+    result =
+      [
+        "withTypeProvider", "addSchema", "addHttpMethod", "addContentTypeParser", "decorate",
+        "decorateRequest", "decorateReply", "setValidatorCompiler", "setSerializerCompiler",
+        "setSchemaController", "setReplySerializer", "setSchemaErrorFormatter", "setErrorHandler",
+        "setNotFoundHandler", "setGenReqId", "setChildLoggerFactory"
+      ]
+  }
+
   /** Gets a data flow node referring to a fastify server. */
   private DataFlow::SourceNode server(DataFlow::SourceNode creation, DataFlow::TypeTracker t) {
     t.start() and
@@ -31,6 +52,11 @@ module Fastify {
     t.start() and
     result = pluginCallback(creation).(DataFlow::FunctionNode).getParameter(0)
     or
+    // server.withTypeProvider<T>(), server.setValidatorCompiler(...), and friends return
+    // the server itself, so the result of such a call still refers to it.
+    t.start() and
+    result = server(creation).getAMethodCall(chainableConfigMethodName())
+    or
     exists(DataFlow::TypeTracker t2 | result = server(creation, t2).track(t2, t))
   }
 
diff --git a/javascript/ql/test/library-tests/frameworks/fastify/src/fastify.js b/javascript/ql/test/library-tests/frameworks/fastify/src/fastify.js
index 8c5264b50e8f..c65b739d726c 100644
--- a/javascript/ql/test/library-tests/frameworks/fastify/src/fastify.js
+++ b/javascript/ql/test/library-tests/frameworks/fastify/src/fastify.js
@@ -90,3 +90,13 @@ fastifyWithObjects4.post(
     request.params;
   }
 );
+
+// the server is reached through a chainable configuration method, which returns the
+// same instance
+var fastifyChained = require("fastify")().withTypeProvider();
+fastifyChained.get(
+  "/",
+  /* handler */ (request, reply) => {
+    reply.send({ hello: "world" }); // response
+  }
+);
diff --git a/javascript/ql/test/library-tests/frameworks/fastify/tests.expected b/javascript/ql/test/library-tests/frameworks/fastify/tests.expected
index a0f2fd1db671..e2b3b303a6ea 100644
--- a/javascript/ql/test/library-tests/frameworks/fastify/tests.expected
+++ b/javascript/ql/test/library-tests/frameworks/fastify/tests.expected
@@ -7,6 +7,7 @@ test_RouteSetup
 | src/fastify.js:63:1:70:1 | fastify ... ;\\n  }\\n) |
 | src/fastify.js:74:1:81:1 | fastify ... ;\\n  }\\n) |
 | src/fastify.js:85:1:92:1 | fastify ... ;\\n  }\\n) |
+| src/fastify.js:97:1:102:1 | fastify ... e\\n  }\\n) |
 test_HeaderAccess
 | src/fastify.js:39:5:39:24 | request.headers.name | name |
 test_RouteHandler
@@ -25,6 +26,7 @@ test_RouteHandler
 | src/fastify.js:65:17:69:3 | functio ... ms;\\n  } | src/fastify.js:61:27:61:46 | require("fastify")() |
 | src/fastify.js:76:17:80:3 | functio ... ms;\\n  } | src/fastify.js:72:27:72:46 | require("fastify")() |
 | src/fastify.js:87:17:91:3 | functio ... ms;\\n  } | src/fastify.js:83:27:83:46 | require("fastify")() |
+| src/fastify.js:99:17:101:3 | (reques ... nse\\n  } | src/fastify.js:96:22:96:41 | require("fastify")() |
 test_HeaderDefinition
 | src/fastify.js:42:5:42:33 | reply.h ... value") | src/fastify.js:34:17:46:3 | functio ... eam\\n  } |
 | src/fastify.js:43:5:43:36 | reply.h ... lue" }) | src/fastify.js:34:17:46:3 | functio ... eam\\n  } |
@@ -34,6 +36,7 @@ test_ServerDefinition
 | src/fastify.js:61:27:61:46 | require("fastify")() |
 | src/fastify.js:72:27:72:46 | require("fastify")() |
 | src/fastify.js:83:27:83:46 | require("fastify")() |
+| src/fastify.js:96:22:96:41 | require("fastify")() |
 test_RedirectInvocation
 | src/fastify.js:44:5:44:29 | reply.r ... e, url) | src/fastify.js:34:17:46:3 | functio ... eam\\n  } |
 test_RequestInputAccess
@@ -57,6 +60,7 @@ test_ResponseSendArgument
 | src/fastify.js:6:12:6:29 | { hello: "world" } | src/fastify.js:5:17:7:3 | async ( ... nse\\n  } |
 | src/fastify.js:27:16:27:33 | { hello: "world" } | src/fastify.js:26:17:28:3 | (reques ... nse\\n  } |
 | src/fastify.js:45:16:45:22 | payload | src/fastify.js:34:17:46:3 | functio ... eam\\n  } |
+| src/fastify.js:100:16:100:33 | { hello: "world" } | src/fastify.js:99:17:101:3 | (reques ... nse\\n  } |
 test_RouteSetup_getServer
 | src/fastify.js:3:1:8:1 | fastify ... e\\n  }\\n) | src/fastify.js:1:15:1:34 | require("fastify")() |
 | src/fastify.js:10:1:21:2 | fastify ... > {}\\n}) | src/fastify.js:1:15:1:34 | require("fastify")() |
@@ -66,6 +70,7 @@ test_RouteSetup_getServer
 | src/fastify.js:63:1:70:1 | fastify ... ;\\n  }\\n) | src/fastify.js:61:27:61:46 | require("fastify")() |
 | src/fastify.js:74:1:81:1 | fastify ... ;\\n  }\\n) | src/fastify.js:72:27:72:46 | require("fastify")() |
 | src/fastify.js:85:1:92:1 | fastify ... ;\\n  }\\n) | src/fastify.js:83:27:83:46 | require("fastify")() |
+| src/fastify.js:97:1:102:1 | fastify ... e\\n  }\\n) | src/fastify.js:96:22:96:41 | require("fastify")() |
 test_HeaderDefinition_defines
 | src/fastify.js:42:5:42:33 | reply.h ... value") | name | value |
 | src/fastify.js:43:5:43:36 | reply.h ... lue" }) | name | value |
@@ -85,6 +90,7 @@ test_RouteSetup_getARouteHandler
 | src/fastify.js:63:1:70:1 | fastify ... ;\\n  }\\n) | src/fastify.js:65:17:69:3 | functio ... ms;\\n  } |
 | src/fastify.js:74:1:81:1 | fastify ... ;\\n  }\\n) | src/fastify.js:76:17:80:3 | functio ... ms;\\n  } |
 | src/fastify.js:85:1:92:1 | fastify ... ;\\n  }\\n) | src/fastify.js:87:17:91:3 | functio ... ms;\\n  } |
+| src/fastify.js:97:1:102:1 | fastify ... e\\n  }\\n) | src/fastify.js:99:17:101:3 | (reques ... nse\\n  } |
 test_RouteHandler_getARequestExpr
 | src/fastify.js:5:17:7:3 | async ( ... nse\\n  } | src/fastify.js:5:24:5:30 | request |
 | src/fastify.js:13:28:13:55 | (reques ... ) => {} | src/fastify.js:13:29:13:35 | request |
@@ -122,6 +128,7 @@ test_RouteHandler_getARequestExpr
 | src/fastify.js:87:17:91:3 | functio ... ms;\\n  } | src/fastify.js:88:5:88:11 | request |
 | src/fastify.js:87:17:91:3 | functio ... ms;\\n  } | src/fastify.js:89:5:89:11 | request |
 | src/fastify.js:87:17:91:3 | functio ... ms;\\n  } | src/fastify.js:90:5:90:11 | request |
+| src/fastify.js:99:17:101:3 | (reques ... nse\\n  } | src/fastify.js:99:18:99:24 | request |
 test_HeaderDefinition_getAHeaderName
 | src/fastify.js:42:5:42:33 | reply.h ... value") | name |
 | src/fastify.js:43:5:43:36 | reply.h ... lue" }) | name |
diff --git a/javascript/ql/test/query-tests/Security/CWE-770/MissingRateLimit/MissingRateLimiting.expected b/javascript/ql/test/query-tests/Security/CWE-770/MissingRateLimit/MissingRateLimiting.expected
index 5e2265f64b49..e8e1be279447 100644
--- a/javascript/ql/test/query-tests/Security/CWE-770/MissingRateLimit/MissingRateLimiting.expected
+++ b/javascript/ql/test/query-tests/Security/CWE-770/MissingRateLimit/MissingRateLimiting.expected
@@ -11,3 +11,5 @@
 | tst.js:88:24:88:40 | expensiveHandler1 | This route handler performs $@, but is not rate-limited. | tst.js:14:40:14:46 | login() | authorization |
 | tst.js:111:28:111:44 | expensiveHandler1 | This route handler performs $@, but is not rate-limited. | tst.js:14:40:14:46 | login() | authorization |
 | tst.js:116:39:116:55 | expensiveHandler1 | This route handler performs $@, but is not rate-limited. | tst.js:14:40:14:46 | login() | authorization |
+| tst.js:130:35:130:51 | expensiveHandler1 | This route handler performs $@, but is not rate-limited. | tst.js:14:40:14:46 | login() | authorization |
+| tst.js:161:35:161:51 | expensiveHandler1 | This route handler performs $@, but is not rate-limited. | tst.js:14:40:14:46 | login() | authorization |
diff --git a/javascript/ql/test/query-tests/Security/CWE-770/MissingRateLimit/tst.js b/javascript/ql/test/query-tests/Security/CWE-770/MissingRateLimit/tst.js
index 7ff0c067fb51..7c5f1708ff6c 100644
--- a/javascript/ql/test/query-tests/Security/CWE-770/MissingRateLimit/tst.js
+++ b/javascript/ql/test/query-tests/Security/CWE-770/MissingRateLimit/tst.js
@@ -116,3 +116,46 @@ const fastifyApp3 = require('fastify')();
 fastifyApp3.get('/before-rate-limit', expensiveHandler1); // $ Alert
 fastifyApp3.register(require('@fastify/rate-limit'));
 fastifyApp3.get('/after-rate-limit', expensiveHandler1);
+
+// the server instance is reached through a chainable configuration method, which
+// returns the same instance
+const fastifyApp4 = require('fastify')().withTypeProvider();
+
+fastifyApp4.register(require('@fastify/rate-limit'));
+fastifyApp4.get('/after-rate-limit', expensiveHandler1);
+
+// same, but with no rate limiter registered at all, so the route is genuinely unguarded
+const fastifyApp5 = require('fastify')().withTypeProvider();
+
+fastifyApp5.get('/no-rate-limit', expensiveHandler1); // $ Alert
+
+// several configuration methods chained together
+const fastifyApp6 = require('fastify')()
+  .withTypeProvider()
+  .setValidatorCompiler(compiler)
+  .addContentTypeParser('application/json', parser)
+  .decorate('answer', 42);
+
+fastifyApp6.register(require('@fastify/rate-limit'));
+fastifyApp6.get('/after-rate-limit', expensiveHandler1);
+
+// the chained instance is returned from a factory function, so reaching it requires
+// tracking the value across the call rather than only through local references
+function makeFastifyApp() {
+  return require('fastify')().withTypeProvider();
+}
+
+const fastifyApp7 = makeFastifyApp();
+
+fastifyApp7.register(require('@fastify/rate-limit'));
+fastifyApp7.get('/after-rate-limit', expensiveHandler1);
+
+// same, from a separate factory so that the server above does not share its creation
+// site, and no rate limiter is registered on it
+function makeUnguardedFastifyApp() {
+  return require('fastify')().withTypeProvider();
+}
+
+const fastifyApp8 = makeUnguardedFastifyApp();
+
+fastifyApp8.get('/no-rate-limit', expensiveHandler1); // $ Alert