diff --git a/cljfmt/src/cljfmt/core.cljc b/cljfmt/src/cljfmt/core.cljc
index 1e9f0e8..bf7fe0e 100644
--- a/cljfmt/src/cljfmt/core.cljc
+++ b/cljfmt/src/cljfmt/core.cljc
@@ -339,11 +339,14 @@
 (defn- make-indenter [[key opts] context]
   (apply some-fn (map (partial indenter-fn key context) opts)))
 
-(defn- indent-order [[key _]]
-  (cond
-    (and (symbol? key) (namespace key)) (str 0 key)
-    (symbol? key) (str 1 key)
-    (pattern? key) (str 2 key)))
+(defn- indent-order [[key specs]]
+  (let [get-depth (fn [[type depth]] (if (= type :inner) depth 0))
+        max-depth (transduce (map get-depth) max 0 specs)
+        key-order  (cond
+                     (qualified-symbol? key) 0
+                     (simple-symbol? key)    1
+                     (pattern? key)          2)]
+    [(- max-depth) key-order (str key)]))
 
 (defn- custom-indent [zloc indents context]
   (if (empty? indents)
diff --git a/cljfmt/test/cljfmt/core_test.cljc b/cljfmt/test/cljfmt/core_test.cljc
index 7721d1e..3f063f8 100644
--- a/cljfmt/test/cljfmt/core_test.cljc
+++ b/cljfmt/test/cljfmt/core_test.cljc
@@ -173,7 +173,40 @@
          ["(defrecord Foo [x]"
           "  Closeable"
           "  (close [_]"
-          "    (prn x)))"])))
+          "    (prn x)))"]))
+    (testing "nested rules like [:inner 1] (#349)"
+      (is (reformats-to?
+           ["(ns my.namespace)"
+            ""
+            "(defprotocol MyProtocol"
+            "MyClass"
+            "(with-x [this x]"
+            "\"with-x is a method\"))"
+            ""
+            "(extend-protocol MyProtocol"
+            "MyClass"
+            "(with-x [this x]"
+            "(+ this x)))"
+            ""
+            "(defn x [x]"
+            "(with-x x "
+            "1))"]
+           ["(ns my.namespace)"
+            ""
+            "(defprotocol MyProtocol"
+            "  MyClass"
+            "  (with-x [this x]"
+            "    \"with-x is a method\"))"
+            ""
+            "(extend-protocol MyProtocol"
+            "  MyClass"
+            "  (with-x [this x]"
+            "    (+ this x)))"
+            ""
+            "(defn x [x]"
+            "  (with-x x"
+            "          1))"]
+           {:extra-indents '{my.namespace/with-x [[:block 0]]}}))))
 
   (testing "data structure indentation"
     (is (reformats-to?