diff --git a/PyInstaller/building/api.py b/PyInstaller/building/api.py
index 5515279899..52afda73ba 100644
--- a/PyInstaller/building/api.py
+++ b/PyInstaller/building/api.py
@@ -840,7 +840,11 @@ def _set_dependencies(self, analysis, path):
                     # relative path needs to be reconstructed from the
                     # name components.
                     if tpl[2] == 'EXTENSION':
-                        ext_components = tpl[0].split('.')[:-1]
+                        # Split on os.path.sep first, to handle additional
+                        # path prefix (e.g., lib-dynload)
+                        ext_components = tpl[0].split(os.path.sep)
+                        ext_components = ext_components[:-1] \
+                            + ext_components[-1].split('.')[:-1]
                         if ext_components:
                             rel_path = os.path.join(*ext_components)
                         else:
diff --git a/PyInstaller/building/build_main.py b/PyInstaller/building/build_main.py
index 7bec0420f1..0fcc1523ec 100644
--- a/PyInstaller/building/build_main.py
+++ b/PyInstaller/building/build_main.py
@@ -480,6 +480,18 @@ def assemble(self):
             self.binding_redirects[:] = list(set(self.binding_redirects))
             logger.info("Found binding redirects: \n%s", self.binding_redirects)
 
+        # Filter binaries to adjust path of extensions that come from
+        # python's lib-dynload directory. Prefix them with lib-dynload
+        # so that we'll collect them into subdirectory instead of
+        # directly into _MEIPASS
+        for idx, tpl in enumerate(self.binaries):
+            name, path, typecode = tpl
+            if typecode == 'EXTENSION' \
+               and not os.path.dirname(os.path.normpath(name)) \
+               and os.path.basename(os.path.dirname(path)) == 'lib-dynload':
+                name = os.path.join('lib-dynload', name)
+                self.binaries[idx] = (name, path, typecode)
+
         # Place Python source in data files for the noarchive case.
         if self.noarchive:
             # Create a new TOC of ``(dest path for .pyc, source for .py, type)``.
diff --git a/news/5583.bugfix.rst b/news/5583.bugfix.rst
new file mode 100644
index 0000000000..dc322e7ae0
--- /dev/null
+++ b/news/5583.bugfix.rst
@@ -0,0 +1 @@
+(OSX) Fix issues with ``pycryptodomex`` on macOS.
diff --git a/news/5604.core.rst b/news/5604.core.rst
new file mode 100644
index 0000000000..b8b0eb7839
--- /dev/null
+++ b/news/5604.core.rst
@@ -0,0 +1,5 @@
+Collect python extension modules that correspond to built-ins into
+``lib-dynload`` sub-directory instead of directly into bundle's root
+directory. This prevents them from shadowing shared libraries with the
+same basename that are located in a package and loaded via ``ctypes`` or
+``cffi``, and also declutters the bundle's root directory.