diff --git a/qiskit/transpiler/passmanager.py b/qiskit/transpiler/passmanager.py
index def19d829a69..ea118c359655 100644
--- a/qiskit/transpiler/passmanager.py
+++ b/qiskit/transpiler/passmanager.py
@@ -169,8 +169,12 @@ def _normalize_passes(
             passes = [passes]
         for pass_ in passes:
             if isinstance(pass_, FlowController):
-                # Normalize passes in nested FlowController
-                PassManager._normalize_passes(pass_.passes)
+                # Normalize passes in nested FlowController.
+                # TODO: Internal renormalisation should be the responsibility of the
+                # `FlowController`, but the separation between `FlowController`,
+                # `RunningPassManager` and `PassManager` is so muddled right now, it would be better
+                # to do this as part of more top-down refactoring.  ---Jake, 2022-10-03.
+                pass_.passes = PassManager._normalize_passes(pass_.passes)
             elif not isinstance(pass_, BasePass):
                 raise TranspilerError(
                     "%s is not a BasePass or FlowController instance " % pass_.__class__
diff --git a/qiskit/transpiler/runningpassmanager.py b/qiskit/transpiler/runningpassmanager.py
index 6cff16cb2c03..036a6d57bc0a 100644
--- a/qiskit/transpiler/runningpassmanager.py
+++ b/qiskit/transpiler/runningpassmanager.py
@@ -181,7 +181,7 @@ def _do_pass(self, pass_, dag, options):
                 pass_.do_while = partial(pass_.do_while, self.fenced_property_set)
 
             for _pass in pass_:
-                self._do_pass(_pass, dag, pass_.options)
+                dag = self._do_pass(_pass, dag, pass_.options)
         else:
             raise TranspilerError(
                 "Expecting type BasePass or FlowController, got %s." % type(pass_)
diff --git a/releasenotes/notes/fix-nested-flow-controllers-a2a5f03eed482fa2.yaml b/releasenotes/notes/fix-nested-flow-controllers-a2a5f03eed482fa2.yaml
new file mode 100644
index 000000000000..b5c719e7382a
--- /dev/null
+++ b/releasenotes/notes/fix-nested-flow-controllers-a2a5f03eed482fa2.yaml
@@ -0,0 +1,8 @@
+---
+fixes:
+  - |
+    Nesting a :class:`.FlowController` inside another in a :class:`.PassManager`
+    could previously cause some transpiler passes to become "forgotten" during
+    transpilation, if the passes returned a new :class:`.DAGCircuit` rather than
+    mutating their input.  Nested :class:`.FlowController`\ s will now affect
+    the transpilation correctly.