diff --git a/HISTORY.rst b/HISTORY.rst
index 9897b738..cc4e0b4a 100644
--- a/HISTORY.rst
+++ b/HISTORY.rst
@@ -12,6 +12,7 @@ PlatformIO 4.0
 * Update SCons tool to 3.1.1
 * Remove ProjectConfig cache when "platformio.ini" was modified outside
 * Fixed an issue with PIO Unified Debugger on Windows OS when debug server is piped
+* Fixed an issue when `--upload-port <http://docs.platformio.org/page/userguide/cmd_run.html#cmdoption-platformio-run-upload-port>`__ CLI flag does not override declared  `upload_port <http://docs.platformio.org/page/projectconf/section_env_upload.html#upload-port>`_ option in `"platformio.ini" (Project Configuration File) <https://docs.platformio.org/page/projectconf.html>`__
 
 4.0.2 (2019-08-23)
 ~~~~~~~~~~~~~~~~~~
diff --git a/platformio/builder/main.py b/platformio/builder/main.py
index f29f2f85..6e5764b3 100644
--- a/platformio/builder/main.py
+++ b/platformio/builder/main.py
@@ -97,6 +97,7 @@ env.Replace(
         for key in list(clivars.keys()) if key in env
     })
 
+
 if env.subst("$BUILDCACHE_DIR"):
     if not isdir(env.subst("$BUILDCACHE_DIR")):
         makedirs(env.subst("$BUILDCACHE_DIR"))
diff --git a/platformio/builder/tools/pioproject.py b/platformio/builder/tools/pioproject.py
index 5797755d..614fb9bd 100644
--- a/platformio/builder/tools/pioproject.py
+++ b/platformio/builder/tools/pioproject.py
@@ -32,7 +32,8 @@ def GetProjectOption(env, option, default=None):
 def LoadProjectOptions(env):
     for option, value in env.GetProjectOptions():
         option_meta = ProjectOptions.get("env." + option)
-        if not option_meta or not option_meta.buildenvvar:
+        if (not option_meta or not option_meta.buildenvvar
+                or option_meta.buildenvvar in env):
             continue
         env[option_meta.buildenvvar] = value