diff --git a/ipykernel/embed.py b/ipykernel/embed.py
index 3e4abd390..ad22e2a1e 100644
--- a/ipykernel/embed.py
+++ b/ipykernel/embed.py
@@ -55,3 +55,4 @@ def embed_kernel(module=None, local_ns=None, **kwargs):
     app.kernel.user_ns = local_ns
     app.shell.set_completer_frame()  # type:ignore[union-attr]
     app.start()
+    app.close()
diff --git a/ipykernel/iostream.py b/ipykernel/iostream.py
index d81710175..ee2b051e6 100644
--- a/ipykernel/iostream.py
+++ b/ipykernel/iostream.py
@@ -595,8 +595,8 @@ def close(self):
             self._should_watch = False
             # thread won't wake unless there's something to read
             # writing something after _should_watch will not be echoed
-            os.write(self._original_stdstream_fd, b"\0")
-            if self.watch_fd_thread is not None:
+            if self.watch_fd_thread is not None and self.watch_fd_thread.is_alive():
+                os.write(self._original_stdstream_fd, b"\0")
                 self.watch_fd_thread.join()
             # restore original FDs
             os.dup2(self._original_stdstream_copy, self._original_stdstream_fd)
diff --git a/ipykernel/kernelapp.py b/ipykernel/kernelapp.py
index 66b750b2b..44e3bafa5 100644
--- a/ipykernel/kernelapp.py
+++ b/ipykernel/kernelapp.py
@@ -397,6 +397,9 @@ def init_heartbeat(self):
         self.heartbeat.start()
 
     def close(self):
+        if self.closed:
+            return
+        self.closed = True
         """Close zmq sockets in an orderly fashion"""
         # un-capture IO before we start closing channels
         self.reset_io()
@@ -471,33 +474,45 @@ def log_connection_info(self):
     def init_blackhole(self):
         """redirects stdout/stderr to devnull if necessary"""
         if self.no_stdout or self.no_stderr:
-            blackhole = open(os.devnull, "w")  # noqa: SIM115
+            # keep reference around so that it would not accidentally close the pipe fds
+            self._blackhole = open(os.devnull, "w")  # noqa: SIM115
             if self.no_stdout:
-                sys.stdout = sys.__stdout__ = blackhole  # type:ignore[misc]
+                if sys.stdout is not None:
+                    sys.stdout.flush()
+                sys.stdout = self._blackhole  # type:ignore[misc]
             if self.no_stderr:
-                sys.stderr = sys.__stderr__ = blackhole  # type:ignore[misc]
+                if sys.stderr is not None:
+                    sys.stderr.flush()
+                sys.stderr = self._blackhole  # type:ignore[misc]
 
     def init_io(self):
         """Redirect input streams and set a display hook."""
         if self.outstream_class:
             outstream_factory = import_item(str(self.outstream_class))
-            if sys.stdout is not None:
-                sys.stdout.flush()
 
-            e_stdout = None if self.quiet else sys.__stdout__
-            e_stderr = None if self.quiet else sys.__stderr__
+            e_stdout = None if self.quiet else sys.stdout
+            e_stderr = None if self.quiet else sys.stderr
 
             if not self.capture_fd_output:
                 outstream_factory = partial(outstream_factory, watchfd=False)
 
+            if sys.stdout is not None:
+                sys.stdout.flush()
             sys.stdout = outstream_factory(self.session, self.iopub_thread, "stdout", echo=e_stdout)
+
             if sys.stderr is not None:
                 sys.stderr.flush()
             sys.stderr = outstream_factory(self.session, self.iopub_thread, "stderr", echo=e_stderr)
+
             if hasattr(sys.stderr, "_original_stdstream_copy"):
                 for handler in self.log.handlers:
-                    if isinstance(handler, StreamHandler) and (handler.stream.buffer.fileno() == 2):
-                        self.log.debug("Seeing logger to stderr, rerouting to raw filedescriptor.")
+                    if (isinstance(handler, StreamHandler)
+                            and (buffer := getattr(handler.stream, "buffer"))
+                            and (fileno := getattr(buffer, "fileno"))
+                            and fileno() == sys.stderr._original_stdstream_fd):
+                        self.log.debug(
+                            "Seeing logger to stderr, rerouting to raw filedescriptor."
+                        )
 
                         handler.stream = TextIOWrapper(
                             FileIO(
@@ -517,9 +532,32 @@ def reset_io(self):
 
         restores state after init_io
         """
-        sys.stdout = sys.__stdout__
-        sys.stderr = sys.__stderr__
-        sys.displayhook = sys.__displayhook__
+        stdout, stderr, displayhook = sys.stdout, sys.stderr, sys.displayhook
+        sys.stdout, sys.stderr, sys.displayhook = self._original_io
+        if (finish_displayhook := getattr(displayhook, "finish_displayhook",
+                                          None)):
+            finish_displayhook()
+        if hasattr(sys.stderr, "_original_stdstream_copy"):
+            for handler in self.log.handlers:
+                if (isinstance(handler, StreamHandler)
+                        and (buffer := getattr(handler.stream, "buffer"))
+                        and (fileno := getattr(buffer, "fileno"))
+                        and fileno() == sys.stderr._original_stdstream_copy):
+                    self.log.debug(
+                        "Seeing logger to raw filedescriptor, rerouting back to stderr"
+                    )
+
+                    handler.stream = TextIOWrapper(
+                        FileIO(
+                            sys.stderr._original_stdstream_fd,
+                            "w",
+                        )
+                    )
+        stderr.close()
+        stdout.close()
+        if self._blackhole:
+            # already closed by above but no harm calling again
+            self._blackhole.close()
 
     def patch_io(self):
         """Patch important libraries that can't handle sys.stdout forwarding"""
@@ -693,6 +731,9 @@ def init_pdb(self):
     @catch_config_error
     def initialize(self, argv=None):
         """Initialize the application."""
+        self.closed = False
+        self._blackhole = None
+        self._original_io = sys.stdout, sys.stderr, sys.displayhook
         self._init_asyncio_patch()
         super().initialize(argv)
         if self.subapp is not None: