diff --git a/spyder/plugins/completion/languageserver/plugin.py b/spyder/plugins/completion/languageserver/plugin.py
index 65753717409..37f5ed7b7c2 100644
--- a/spyder/plugins/completion/languageserver/plugin.py
+++ b/spyder/plugins/completion/languageserver/plugin.py
@@ -26,6 +26,7 @@
 from spyder.config.manager import CONF
 from spyder.api.completion import SpyderCompletionPlugin
 from spyder.utils.misc import check_connection_port, getcwd_or_home
+from spyder.utils.programs import get_python_site_packages
 from spyder.plugins.completion.languageserver import LSP_LANGUAGES
 from spyder.plugins.completion.languageserver.client import LSPClient
 from spyder.plugins.completion.languageserver.confpage import (
@@ -574,15 +575,20 @@ def generate_python_config(self):
         }
 
         # Jedi configuration
+        extra_paths = self.get_option('spyder_pythonpath', section='main',
+                                      default=[])
         if self.get_option('default', section='main_interpreter'):
             environment = None
         else:
             environment = self.get_option('custom_interpreter',
                                           section='main_interpreter')
+            # jedi can miss the site-package: see
+            # https://github.com/davidhalter/jedi/issues/1540
+            extra_paths += get_python_site_packages(environment)
+
         jedi = {
             'environment': environment,
-            'extra_paths': self.get_option('spyder_pythonpath',
-                                           section='main', default=[]),
+            'extra_paths': extra_paths,
         }
         jedi_completion = {
             'enabled': self.get_option('code_completion'),
diff --git a/spyder/utils/programs.py b/spyder/utils/programs.py
index 5f8509131df..65e0c471782 100644
--- a/spyder/utils/programs.py
+++ b/spyder/utils/programs.py
@@ -24,6 +24,7 @@
 import tempfile
 import threading
 import time
+import ast
 
 # Third party imports
 import psutil
@@ -967,6 +968,19 @@ def check_python_help(filename):
         return False
 
 
+def get_python_site_packages(pyexec):
+    """Get the site-packages for a given python executable"""
+    script = 'import site; print(site.getsitepackages())'
+    try:
+        proc = run_program('env', ['-i', pyexec, '-c', script])
+        stdout, stderr = proc.communicate()
+        pkgs = ast.literal_eval(stdout.decode())
+    except Exception:
+        pkgs = []
+
+    return pkgs
+
+
 def is_spyder_process(pid):
     """
     Test whether given PID belongs to a Spyder process.