diff --git a/news/2849.bugfix b/news/2849.bugfix
new file mode 100644
index 0000000000..65fda3e3fa
--- /dev/null
+++ b/news/2849.bugfix
@@ -0,0 +1 @@
+Fixed a bug in ``pipenv clean`` which caused global packages to sometimes be inadvertently targeted for cleanup.
diff --git a/pipenv/core.py b/pipenv/core.py
index cc4ba51f05..5a1a997960 100644
--- a/pipenv/core.py
+++ b/pipenv/core.py
@@ -2327,8 +2327,6 @@ def do_check(
 
 def do_graph(bare=False, json=False, json_tree=False, reverse=False):
     import pipdeptree
-
-
     try:
         python_path = which("python")
     except AttributeError:
@@ -2390,7 +2388,7 @@ def do_graph(bare=False, json=False, json_tree=False, reverse=False):
             err=True,
         )
         sys.exit(1)
-    cmd = '"{0}" {1} {2}'.format(
+    cmd = '"{0}" {1} {2} -l'.format(
         python_path, escape_grouped_arguments(pipdeptree.__file__.rstrip("cdo")), flag
     )
     # Run dep-tree.
diff --git a/pipenv/project.py b/pipenv/project.py
index 0722619f1d..1a371fdae5 100644
--- a/pipenv/project.py
+++ b/pipenv/project.py
@@ -9,6 +9,7 @@
 import hashlib
 import contoml
 from first import first
+from cached_property import cached_property
 import pipfile
 import pipfile.api
 import six
@@ -279,26 +280,44 @@ def get_location_for_virtualenv(self):
                     return vistir.compat.Path(name).absolute().as_posix()
         return str(get_workon_home().joinpath(name))
 
-    def get_installed_packages(self):
-        from . import PIPENV_ROOT, PIPENV_VENDOR, PIPENV_PATCHED
-        from .utils import temp_path, load_path, temp_environ
+    @property
+    def working_set(self):
+        from .utils import load_path
+        sys_path = load_path(self.which("python"))
+        import pkg_resources
+        return pkg_resources.WorkingSet(sys_path)
+
+    def find_egg(self, egg_dist):
+        import site
+        from distutils import sysconfig as distutils_sysconfig
+        site_packages = distutils_sysconfig.get_python_lib()
+        search_filename = "{0}.egg-link".format(egg_dist.project_name)
+        try:
+            user_site = site.getusersitepackages()
+        except AttributeError:
+            user_site = site.USER_SITE
+        search_locations = [site_packages, user_site]
+        for site_directory in search_locations:
+                egg = os.path.join(site_directory, search_filename)
+                if os.path.isfile(egg):
+                    return egg
+
+    def locate_dist(self, dist):
+        location = self.find_egg(dist)
+        if not location:
+            return dist.location
 
+    def get_installed_packages(self):
+        workingset = self.working_set
+        prefix = _normalized(self.env_paths["prefix"])
         if self.virtualenv_exists:
-            with temp_path(), temp_environ():
-                new_path = load_path(self.which("python"))
-                new_path = [
-                    new_path[0],
-                    PIPENV_ROOT,
-                    PIPENV_PATCHED,
-                    PIPENV_VENDOR,
-                ] + new_path[1:]
-                sys.path = new_path
-                os.environ["VIRTUAL_ENV"] = self.virtualenv_location
-                from .vendor.pip_shims.shims import get_installed_distributions
-
-                return get_installed_distributions(local_only=True)
+            packages = [
+                pkg for pkg in workingset
+                if _normalized(self.locate_dist(pkg)).startswith(prefix)
+            ]
+            return packages
         else:
-            return []
+            return [pkg for pkg in packages]
 
     @classmethod
     def _sanitize(cls, name):
@@ -902,3 +921,34 @@ def proper_case_section(self, section):
                 del section[dep]
         # Return whether or not values have been changed.
         return changed_values
+
+    @property
+    def _pyversion(self):
+        include_dir = vistir.compat.Path(self.virtualenv_location) / "include"
+        python_path = next(iter(list(include_dir.iterdir())), None)
+        if python_path and python_path.name.startswith("python"):
+            python_version = python_path.name.replace("python", "")
+            py_version_short, abiflags = python_version[:3], python_version[3:]
+            return {"py_version_short": py_version_short, "abiflags": abiflags}
+        return {}
+
+    @property
+    def env_paths(self):
+        import sysconfig
+        location = self.virtualenv_location if self.virtualenv_location else sys.prefix
+        prefix = vistir.compat.Path(location).as_posix()
+        scheme = sysconfig._get_default_scheme()
+        config = {
+            "base": prefix,
+            "installed_base": prefix,
+            "platbase": prefix,
+            "installed_platbase": prefix
+        }
+        config.update(self._pyversion)
+        paths = {
+            k: v.format(**config)
+            for k, v in sysconfig._INSTALL_SCHEMES[scheme].items()
+        }
+        if "prefix" not in paths:
+            paths["prefix"] = prefix
+        return paths