commit https://github.com/vim/vim/commit/1000565c3a2439c9a7c9759284814dbf3b8bc20d Author: Bram Moolenaar <Bram@vim.org> Date: Thu Dec 31 21:03:23 2015 +0100 patch 7.4.1012 Problem: Vim overwrites the value of $PYTHONHOME. Solution: Do not set $PYTHONHOME if it is already set. (Kazuki Sakamoto, closes https://github.com/vim/vim/issues/500)

--- a/src/if_python3.c
+++ b/src/if_python3.c
@@ -858,7 +858,10 @@ Python3_Init(void)
 
 
 #ifdef PYTHON3_HOME
-	Py_SetPythonHome(PYTHON3_HOME);
+# ifdef DYNAMIC_PYTHON3
+	if (mch_getenv((char_u *)"PYTHONHOME") == NULL)
+# endif
+	    Py_SetPythonHome(PYTHON3_HOME);
 #endif
 
 	PyImport_AppendInittab("vim", Py3Init_vim);