diff --git a/changelog/3747.bugfix.rst b/changelog/3747.bugfix.rst
new file mode 100644
index 00000000000..a9123f25535
--- /dev/null
+++ b/changelog/3747.bugfix.rst
@@ -0,0 +1 @@
+Fix compatibility problem with plugins and the warning code issued by fixture functions when they are called directly.
diff --git a/src/_pytest/compat.py b/src/_pytest/compat.py
index a1cd3bd4ed4..52051ff2326 100644
--- a/src/_pytest/compat.py
+++ b/src/_pytest/compat.py
@@ -249,6 +249,21 @@ def get_real_func(obj):
     return obj
 
 
+def get_real_method(obj, holder):
+    """
+    Attempts to obtain the real function object that might be wrapping ``obj``, while at the same time
+    returning a bound method to ``holder`` if the original object was a bound method.
+    """
+    try:
+        is_method = hasattr(obj, "__func__")
+        obj = get_real_func(obj)
+    except Exception:
+        return obj
+    if is_method and hasattr(obj, "__get__") and callable(obj.__get__):
+        obj = obj.__get__(holder)
+    return obj
+
+
 def getfslineno(obj):
     # xxx let decorators etc specify a sane ordering
     obj = get_real_func(obj)
diff --git a/src/_pytest/fixtures.py b/src/_pytest/fixtures.py
index 93557fa04eb..818c5b81f74 100644
--- a/src/_pytest/fixtures.py
+++ b/src/_pytest/fixtures.py
@@ -30,6 +30,7 @@
     getfuncargnames,
     safe_getattr,
     FuncargnamesCompatAttr,
+    get_real_method,
 )
 from _pytest.deprecated import FIXTURE_FUNCTION_CALL, RemovedInPytest4Warning
 from _pytest.outcomes import fail, TEST_OUTCOME
@@ -931,13 +932,6 @@ def pytest_fixture_setup(fixturedef, request):
         request._check_scope(argname, request.scope, fixdef.scope)
         kwargs[argname] = result
 
-    # if function has been defined with @pytest.fixture, we want to
-    # pass the special __being_called_by_pytest parameter so we don't raise a warning
-    # this is an ugly hack, see #3720 for an opportunity to improve this
-    defined_using_fixture_decorator = hasattr(fixturedef.func, "_pytestfixturefunction")
-    if defined_using_fixture_decorator:
-        kwargs["__being_called_by_pytest"] = True
-
     fixturefunc = resolve_fixture_function(fixturedef, request)
     my_cache_key = request.param_index
     try:
@@ -973,9 +967,7 @@ def wrap_function_to_warning_if_called_directly(function, fixture_marker):
         @functools.wraps(function)
         def result(*args, **kwargs):
             __tracebackhide__ = True
-            __being_called_by_pytest = kwargs.pop("__being_called_by_pytest", False)
-            if not __being_called_by_pytest:
-                warnings.warn(warning, stacklevel=3)
+            warnings.warn(warning, stacklevel=3)
             for x in function(*args, **kwargs):
                 yield x
 
@@ -984,9 +976,7 @@ def result(*args, **kwargs):
         @functools.wraps(function)
         def result(*args, **kwargs):
             __tracebackhide__ = True
-            __being_called_by_pytest = kwargs.pop("__being_called_by_pytest", False)
-            if not __being_called_by_pytest:
-                warnings.warn(warning, stacklevel=3)
+            warnings.warn(warning, stacklevel=3)
             return function(*args, **kwargs)
 
     if six.PY2:
@@ -1279,9 +1269,9 @@ def parsefactories(self, node_or_obj, nodeid=NOTSET, unittest=False):
             # The attribute can be an arbitrary descriptor, so the attribute
             # access below can raise. safe_getatt() ignores such exceptions.
             obj = safe_getattr(holderobj, name, None)
+            marker = getfixturemarker(obj)
             # fixture functions have a pytest_funcarg__ prefix (pre-2.3 style)
             # or are "@pytest.fixture" marked
-            marker = getfixturemarker(obj)
             if marker is None:
                 if not name.startswith(self._argprefix):
                     continue
@@ -1303,6 +1293,15 @@ def parsefactories(self, node_or_obj, nodeid=NOTSET, unittest=False):
                     name = marker.name
                 assert not name.startswith(self._argprefix), FIXTURE_MSG.format(name)
 
+            # during fixture definition we wrap the original fixture function
+            # to issue a warning if called directly, so here we unwrap it in order to not emit the warning
+            # when pytest itself calls the fixture function
+            if six.PY2 and unittest:
+                # hack on Python 2 because of the unbound methods
+                obj = get_real_func(obj)
+            else:
+                obj = get_real_method(obj, holderobj)
+
             fixture_def = FixtureDef(
                 self,
                 nodeid,
diff --git a/testing/deprecated_test.py b/testing/deprecated_test.py
index 2a9b4be9135..41907503e8a 100644
--- a/testing/deprecated_test.py
+++ b/testing/deprecated_test.py
@@ -267,7 +267,6 @@ def test_func():
     )
 
 
-# @pytest.mark.skipif(six.PY2, reason="We issue the warning in Python 3 only")
 def test_call_fixture_function_deprecated():
     """Check if a warning is raised if a fixture function is called directly (#3661)"""
 
diff --git a/testing/python/fixture.py b/testing/python/fixture.py
index 70d79ab7132..a3c6b95b095 100644
--- a/testing/python/fixture.py
+++ b/testing/python/fixture.py
@@ -1470,10 +1470,9 @@ def test_hello(self, item, fm):
                     print (faclist)
                     assert len(faclist) == 3
 
-                    kwargs = {'__being_called_by_pytest': True}
-                    assert faclist[0].func(item._request, **kwargs) == "conftest"
-                    assert faclist[1].func(item._request, **kwargs) == "module"
-                    assert faclist[2].func(item._request, **kwargs) == "class"
+                    assert faclist[0].func(item._request) == "conftest"
+                    assert faclist[1].func(item._request) == "module"
+                    assert faclist[2].func(item._request) == "class"
         """
         )
         reprec = testdir.inline_run("-s")