diff --git a/changelog/3616.deprecation.rst b/changelog/3616.deprecation.rst
new file mode 100644
index 00000000000..8ea1b4d3d14
--- /dev/null
+++ b/changelog/3616.deprecation.rst
@@ -0,0 +1,22 @@
+The following accesses have been documented as deprecated for years, but are now actually emitting deprecation warnings.
+
+* Access of ``Module``, ``Function``, ``Class``, ``Instance``, ``File`` and ``Item`` through ``Node`` instances. Now
+  users will this warning::
+
+        usage of Function.Module is deprecated, please use pytest.Module instead
+
+  Users should just ``import pytest`` and access those objects using the ``pytest`` module.
+
+* ``request.cached_setup``, this was the precursor of the setup/teardown mechanism available to fixtures. You can
+  consult `funcarg comparision section in the docs <https://docs.pytest.org/en/latest/funcarg_compare.html>`_.
+
+* Using objects named ``"Class"`` as a way to customize the type of nodes that are collected in ``Collector``
+  subclasses has been deprecated. Users instead should use ``pytest_collect_make_item`` to customize node types during
+  collection.
+
+  This issue should affect only advanced plugins who create new collection types, so if you see this warning
+  message please contact the authors so they can change the code.
+
+* The warning that produces the message below has changed to ``RemovedInPytest4Warning``::
+
+        getfuncargvalue is deprecated, use getfixturevalue
diff --git a/changelog/README.rst b/changelog/README.rst
index 47e21fb33fb..e471409b023 100644
--- a/changelog/README.rst
+++ b/changelog/README.rst
@@ -14,7 +14,8 @@ Each file should be named like ``<ISSUE>.<TYPE>.rst``, where
 * ``feature``: new user facing features, like new command-line options and new behavior.
 * ``bugfix``: fixes a reported bug.
 * ``doc``: documentation improvement, like rewording an entire session or adding missing docs.
-* ``removal``: feature deprecation or removal.
+* ``deprecation``: feature deprecation.
+* ``removal``: feature removal.
 * ``vendor``: changes in packages vendored in pytest.
 * ``trivial``: fixing a small typo or internal change that might be noteworthy.
 
diff --git a/doc/en/historical-notes.rst b/doc/en/historical-notes.rst
index 028ceff9b17..9462d700f26 100644
--- a/doc/en/historical-notes.rst
+++ b/doc/en/historical-notes.rst
@@ -175,3 +175,13 @@ Previous to version 2.4 to set a break point in code one needed to use ``pytest.
 This is no longer needed and one can use the native ``import pdb;pdb.set_trace()`` call directly.
 
 For more details see :ref:`breakpoints`.
+
+"compat" properties
+-------------------
+
+.. deprecated:: 3.9
+
+Access of ``Module``, ``Function``, ``Class``, ``Instance``, ``File`` and ``Item`` through ``Node`` instances have long
+been documented as deprecated, but started to emit warnings from pytest ``3.9`` and onward.
+
+Users should just ``import pytest`` and access those objects using the ``pytest`` module.
diff --git a/pyproject.toml b/pyproject.toml
index b1e85601ec5..e82f051e1d4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -15,7 +15,12 @@ template = "changelog/_template.rst"
 
   [[tool.towncrier.type]]
   directory = "removal"
-  name = "Deprecations and Removals"
+  name = "Removals"
+  showcontent = true
+
+  [[tool.towncrier.type]]
+  directory = "deprecation"
+  name = "Deprecations"
   showcontent = true
 
   [[tool.towncrier.type]]
diff --git a/src/_pytest/config/findpaths.py b/src/_pytest/config/findpaths.py
index 7480603bece..f994301988f 100644
--- a/src/_pytest/config/findpaths.py
+++ b/src/_pytest/config/findpaths.py
@@ -103,21 +103,18 @@ def determine_setup(inifile, args, rootdir_cmd_arg=None, config=None):
     if inifile:
         iniconfig = py.iniconfig.IniConfig(inifile)
         is_cfg_file = str(inifile).endswith(".cfg")
-        # TODO: [pytest] section in *.cfg files is depricated. Need refactoring.
         sections = ["tool:pytest", "pytest"] if is_cfg_file else ["pytest"]
         for section in sections:
             try:
                 inicfg = iniconfig[section]
                 if is_cfg_file and section == "pytest" and config is not None:
                     from _pytest.deprecated import CFG_PYTEST_SECTION
-                    from _pytest.warning_types import RemovedInPytest4Warning
                     from _pytest.warnings import _issue_config_warning
 
+                    # TODO: [pytest] section in *.cfg files is deprecated. Need refactoring once
+                    # the deprecation expires.
                     _issue_config_warning(
-                        RemovedInPytest4Warning(
-                            CFG_PYTEST_SECTION.format(filename=str(inifile))
-                        ),
-                        config,
+                        CFG_PYTEST_SECTION.format(filename=str(inifile)), config
                     )
                 break
             except KeyError:
diff --git a/src/_pytest/deprecated.py b/src/_pytest/deprecated.py
index dea8bbde867..69beeab5f91 100644
--- a/src/_pytest/deprecated.py
+++ b/src/_pytest/deprecated.py
@@ -4,10 +4,15 @@
 
 Keeping it in a central location makes it easy to track what is deprecated and should
 be removed when the time comes.
+
+All constants defined in this module should be either PytestWarning instances or UnformattedWarning
+in case of warnings which need to format their messages.
 """
 from __future__ import absolute_import, division, print_function
 
-from _pytest.warning_types import RemovedInPytest4Warning
+
+from _pytest.warning_types import UnformattedWarning, RemovedInPytest4Warning
+
 
 MAIN_STR_ARGS = RemovedInPytest4Warning(
     "passing a string to pytest.main() is deprecated, "
@@ -18,25 +23,48 @@
     "yield tests are deprecated, and scheduled to be removed in pytest 4.0"
 )
 
-FUNCARG_PREFIX = (
+CACHED_SETUP = RemovedInPytest4Warning(
+    "cached_setup is deprecated and will be removed in a future release. "
+    "Use standard fixture functions instead."
+)
+
+COMPAT_PROPERTY = UnformattedWarning(
+    RemovedInPytest4Warning,
+    "usage of {owner}.{name} is deprecated, please use pytest.{name} instead",
+)
+
+CUSTOM_CLASS = UnformattedWarning(
+    RemovedInPytest4Warning,
+    'use of special named "{name}" objects in collectors of type "{type_name}" to '
+    "customize the created nodes is deprecated. "
+    "Use pytest_pycollect_makeitem(...) to create custom "
+    "collection nodes instead.",
+)
+
+FUNCARG_PREFIX = UnformattedWarning(
+    RemovedInPytest4Warning,
     '{name}: declaring fixtures using "pytest_funcarg__" prefix is deprecated '
     "and scheduled to be removed in pytest 4.0.  "
-    "Please remove the prefix and use the @pytest.fixture decorator instead."
+    "Please remove the prefix and use the @pytest.fixture decorator instead.",
 )
 
-FIXTURE_FUNCTION_CALL = (
+FIXTURE_FUNCTION_CALL = UnformattedWarning(
+    RemovedInPytest4Warning,
     'Fixture "{name}" called directly. Fixtures are not meant to be called directly, '
     "are created automatically when test functions request them as parameters. "
-    "See https://docs.pytest.org/en/latest/fixture.html for more information."
+    "See https://docs.pytest.org/en/latest/fixture.html for more information.",
 )
 
-CFG_PYTEST_SECTION = (
-    "[pytest] section in {filename} files is deprecated, use [tool:pytest] instead."
+CFG_PYTEST_SECTION = UnformattedWarning(
+    RemovedInPytest4Warning,
+    "[pytest] section in {filename} files is deprecated, use [tool:pytest] instead.",
 )
 
-GETFUNCARGVALUE = "getfuncargvalue is deprecated, use getfixturevalue"
+GETFUNCARGVALUE = RemovedInPytest4Warning(
+    "getfuncargvalue is deprecated, use getfixturevalue"
+)
 
-RESULT_LOG = (
+RESULT_LOG = RemovedInPytest4Warning(
     "--result-log is deprecated and scheduled for removal in pytest 4.0.\n"
     "See https://docs.pytest.org/en/latest/usage.html#creating-resultlog-format-files for more information."
 )
diff --git a/src/_pytest/fixtures.py b/src/_pytest/fixtures.py
index 068e6814c1d..964b16e2997 100644
--- a/src/_pytest/fixtures.py
+++ b/src/_pytest/fixtures.py
@@ -32,7 +32,7 @@
     get_real_method,
     _PytestWrapper,
 )
-from _pytest.deprecated import FIXTURE_FUNCTION_CALL, RemovedInPytest4Warning
+from _pytest.deprecated import FIXTURE_FUNCTION_CALL
 from _pytest.outcomes import fail, TEST_OUTCOME
 
 FIXTURE_MSG = 'fixtures cannot have "pytest_funcarg__" prefix and be decorated with @pytest.fixture:\n{}'
@@ -479,6 +479,9 @@ def cached_setup(self, setup, teardown=None, scope="module", extrakey=None):
             or ``session`` indicating the caching lifecycle of the resource.
         :arg extrakey: added to internal caching key of (funcargname, scope).
         """
+        from _pytest.deprecated import CACHED_SETUP
+
+        warnings.warn(CACHED_SETUP, stacklevel=2)
         if not hasattr(self.config, "_setupcache"):
             self.config._setupcache = {}  # XXX weakref?
         cachekey = (self.fixturename, self._getscopeitem(scope), extrakey)
@@ -512,7 +515,7 @@ def getfuncargvalue(self, argname):
         """ Deprecated, use getfixturevalue. """
         from _pytest import deprecated
 
-        warnings.warn(deprecated.GETFUNCARGVALUE, DeprecationWarning, stacklevel=2)
+        warnings.warn(deprecated.GETFUNCARGVALUE, stacklevel=2)
         return self.getfixturevalue(argname)
 
     def _get_active_fixturedef(self, argname):
@@ -956,8 +959,9 @@ def wrap_function_to_warning_if_called_directly(function, fixture_marker):
     used as an argument in a test function.
     """
     is_yield_function = is_generator(function)
-    msg = FIXTURE_FUNCTION_CALL.format(name=fixture_marker.name or function.__name__)
-    warning = RemovedInPytest4Warning(msg)
+    warning = FIXTURE_FUNCTION_CALL.format(
+        name=fixture_marker.name or function.__name__
+    )
 
     if is_yield_function:
 
@@ -1284,9 +1288,7 @@ def parsefactories(self, node_or_obj, nodeid=NOTSET, unittest=False):
 
                 filename, lineno = getfslineno(obj)
                 warnings.warn_explicit(
-                    RemovedInPytest4Warning(
-                        deprecated.FUNCARG_PREFIX.format(name=name)
-                    ),
+                    deprecated.FUNCARG_PREFIX.format(name=name),
                     category=None,
                     filename=str(filename),
                     lineno=lineno + 1,
diff --git a/src/_pytest/nodes.py b/src/_pytest/nodes.py
index 29d1f0a871b..9cd7589415c 100644
--- a/src/_pytest/nodes.py
+++ b/src/_pytest/nodes.py
@@ -61,11 +61,11 @@ def __get__(self, obj, owner):
         if obj is None:
             return self
 
-        # TODO: reenable in the features branch
-        # warnings.warn(
-        #     "usage of {owner!r}.{name} is deprecated, please use pytest.{name} instead".format(
-        #         name=self.name, owner=type(owner).__name__),
-        #     PendingDeprecationWarning, stacklevel=2)
+        from _pytest.deprecated import COMPAT_PROPERTY
+
+        warnings.warn(
+            COMPAT_PROPERTY.format(name=self.name, owner=owner.__name__), stacklevel=2
+        )
         return getattr(__import__("pytest"), self.name)
 
 
@@ -126,11 +126,10 @@ def _getcustomclass(self, name):
         if isinstance(maybe_compatprop, _CompatProperty):
             return getattr(__import__("pytest"), name)
         else:
+            from _pytest.deprecated import CUSTOM_CLASS
+
             cls = getattr(self, name)
-            # TODO: reenable in the features branch
-            # warnings.warn("use of node.%s is deprecated, "
-            #    "use pytest_pycollect_makeitem(...) to create custom "
-            #    "collection nodes" % name, category=DeprecationWarning)
+            self.warn(CUSTOM_CLASS.format(name=name, type_name=type(self).__name__))
         return cls
 
     def __repr__(self):
diff --git a/src/_pytest/python.py b/src/_pytest/python.py
index 05165027231..a0a0655fd65 100644
--- a/src/_pytest/python.py
+++ b/src/_pytest/python.py
@@ -800,7 +800,10 @@ def collect(self):
                     "%r generated tests with non-unique name %r" % (self, name)
                 )
             seen[name] = True
-            values.append(self.Function(name, self, args=args, callobj=call))
+            with warnings.catch_warnings():
+                # ignore our own deprecation warning
+                function_class = self.Function
+            values.append(function_class(name, self, args=args, callobj=call))
         self.warn(deprecated.YIELD_TESTS)
         return values
 
diff --git a/src/_pytest/resultlog.py b/src/_pytest/resultlog.py
index 8a972eed736..9ae90e7704a 100644
--- a/src/_pytest/resultlog.py
+++ b/src/_pytest/resultlog.py
@@ -31,10 +31,9 @@ def pytest_configure(config):
         config.pluginmanager.register(config._resultlog)
 
         from _pytest.deprecated import RESULT_LOG
-        from _pytest.warning_types import RemovedInPytest4Warning
         from _pytest.warnings import _issue_config_warning
 
-        _issue_config_warning(RemovedInPytest4Warning(RESULT_LOG), config)
+        _issue_config_warning(RESULT_LOG, config)
 
 
 def pytest_unconfigure(config):
diff --git a/src/_pytest/warning_types.py b/src/_pytest/warning_types.py
index 8861f6f2b06..55e1f037ae5 100644
--- a/src/_pytest/warning_types.py
+++ b/src/_pytest/warning_types.py
@@ -1,3 +1,6 @@
+import attr
+
+
 class PytestWarning(UserWarning):
     """
     Bases: :class:`UserWarning`.
@@ -39,4 +42,19 @@ def simple(cls, apiname):
         )
 
 
+@attr.s
+class UnformattedWarning(object):
+    """Used to hold warnings that need to format their message at runtime, as opposed to a direct message.
+
+    Using this class avoids to keep all the warning types and messages in this module, avoiding misuse.
+    """
+
+    category = attr.ib()
+    template = attr.ib()
+
+    def format(self, **kwargs):
+        """Returns an instance of the warning category, formatted with given kwargs"""
+        return self.category(self.template.format(**kwargs))
+
+
 PYTESTER_COPY_EXAMPLE = PytestExperimentalApiWarning.simple("testdir.copy_example")
diff --git a/testing/deprecated_test.py b/testing/deprecated_test.py
index fbaca4e30fd..49b21ccb1b8 100644
--- a/testing/deprecated_test.py
+++ b/testing/deprecated_test.py
@@ -30,6 +30,74 @@ def test_gen2():
     assert result.stdout.str().count("yield tests are deprecated") == 2
 
 
+def test_compat_properties_deprecation(testdir):
+    testdir.makepyfile(
+        """
+        def test_foo(request):
+            print(request.node.Module)
+    """
+    )
+    result = testdir.runpytest()
+    result.stdout.fnmatch_lines(
+        [
+            "*test_compat_properties_deprecation.py:2:*usage of Function.Module is deprecated, "
+            "please use pytest.Module instead*",
+            "*1 passed, 1 warnings in*",
+        ]
+    )
+
+
+def test_cached_setup_deprecation(testdir):
+    testdir.makepyfile(
+        """
+        import pytest
+        @pytest.fixture
+        def fix(request):
+            return request.cached_setup(lambda: 1)
+
+        def test_foo(fix):
+            assert fix == 1
+    """
+    )
+    result = testdir.runpytest()
+    result.stdout.fnmatch_lines(
+        [
+            "*test_cached_setup_deprecation.py:4:*cached_setup is deprecated*",
+            "*1 passed, 1 warnings in*",
+        ]
+    )
+
+
+def test_custom_class_deprecation(testdir):
+    testdir.makeconftest(
+        """
+        import pytest
+
+        class MyModule(pytest.Module):
+
+            class Class(pytest.Class):
+                pass
+
+        def pytest_pycollect_makemodule(path, parent):
+            return MyModule(path, parent)
+    """
+    )
+    testdir.makepyfile(
+        """
+        class Test:
+            def test_foo(self):
+                pass
+    """
+    )
+    result = testdir.runpytest()
+    result.stdout.fnmatch_lines(
+        [
+            '*test_custom_class_deprecation.py:1:*"Class" objects in collectors of type "MyModule*',
+            "*1 passed, 1 warnings in*",
+        ]
+    )
+
+
 @pytest.mark.filterwarnings("default")
 def test_funcarg_prefix_deprecation(testdir):
     testdir.makepyfile(
diff --git a/testing/python/collect.py b/testing/python/collect.py
index c92de12a09c..25d8a8e779d 100644
--- a/testing/python/collect.py
+++ b/testing/python/collect.py
@@ -240,6 +240,9 @@ def prop(self):
         assert result.ret == EXIT_NOTESTSCOLLECTED
 
 
+@pytest.mark.filterwarnings(
+    "ignore:usage of Generator.Function is deprecated, please use pytest.Function instead"
+)
 class TestGenerator(object):
     def test_generative_functions(self, testdir):
         modcol = testdir.getmodulecol(
@@ -1255,6 +1258,9 @@ def test_hello(self): pass
         assert lineno == 1
         assert msg == "TestClass"
 
+    @pytest.mark.filterwarnings(
+        "ignore:usage of Generator.Function is deprecated, please use pytest.Function instead"
+    )
     def test_generator_reportinfo(self, testdir):
         modcol = testdir.getmodulecol(
             """
diff --git a/testing/python/fixture.py b/testing/python/fixture.py
index fc3eee42b5f..4e44bf9611f 100644
--- a/testing/python/fixture.py
+++ b/testing/python/fixture.py
@@ -977,6 +977,7 @@ def test_func2b(self, something):
         )
         reprec.assertoutcome(passed=4)
 
+    @pytest.mark.filterwarnings("ignore:cached_setup is deprecated")
     def test_request_cachedsetup_extrakey(self, testdir):
         item1 = testdir.getitem("def test_func(): pass")
         req1 = fixtures.FixtureRequest(item1)
@@ -994,6 +995,7 @@ def setup():
         assert ret1 == ret1b
         assert ret2 == ret2b
 
+    @pytest.mark.filterwarnings("ignore:cached_setup is deprecated")
     def test_request_cachedsetup_cache_deletion(self, testdir):
         item1 = testdir.getitem("def test_func(): pass")
         req1 = fixtures.FixtureRequest(item1)