subprocess seems not working in pyinstaller exe file

Problem was solved by not using -w command for generating exe file from .py script.

Use this function to get the command's output instead. Works with -F and -w option:

import subprocess
def popen(cmd: str) -> str:
    """For pyinstaller -w"""
    startupinfo = subprocess.STARTUPINFO()
    startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW
    process = subprocess.Popen(cmd,startupinfo=startupinfo, stdout=subprocess.PIPE, stderr=subprocess.PIPE, stdin=subprocess.PIPE)
    return decode_utf8_fixed(process.stdout.read())

You can compile your code in -w mode or --windowed, but then you have to assign stdin and stderr as well.

So change:

s = subprocess.Popen([EXE,files,'command'],shell=True, stdout=subprocess.PIPE)

to:

s = subprocess.Popen([EXE,files,'command'],shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE, stdin=subprocess.PIPE)