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[bo8ster]

Taken from here. I hope this will help people understand the functions used more.
This works using two scripts, one is your normal script you want to capture the output from and the other is used to capture the output.
I have used a msgbox but you can replace that with a FileWrite.

Script One - My custom script where I want to save the output. Fancy I know! Note comments are not written using #AutoIt3Wrapper_Run_Debug_Mode=Y

#AutoIt3Wrapper_Run_Debug_Mode=Y
AutoItSetOption("SendKeyDelay", 90);
AutoItSetOption("MustDeclareVars", 1)

ConsoleWrite(@CRLF & @CRLF & " Hello world" & @CRLF & " This is a test" & @CRLF & @CRLF)

;~ End of script
Exit

Script Two - Used to execute and capture the output of Script One. Most of it I copied from the help file. The run cmd I got from Scite when Pressing F5. I believe everything comes from STDOUT so STDERR is not really required but its there. Using this $line can be written to a file if required.

#include <Constants.au3>

Local $foo = Run('"C:\Program Files\AutoIt3\SciTE\AutoIt3Wrapper\AutoIt3Wrapper.exe" /run /prod /ErrorStdOut /in "C:\<....>\workspace.au3" /autoit3dir "C:\Program Files\AutoIt3" /UserParams', @SystemDir, @SW_HIDE, $STDERR_CHILD + $STDOUT_CHILD)

Local $line
While 1
    ProcessWaitClose($foo)
    $line = StdoutRead($foo)
    If @error Then ExitLoop
    MsgBox(0, "STDOUT read:", $line)
    
Wend

While 1
    ProcessWaitClose($foo)
    $line = StderrRead($foo)
    If @error Then ExitLoop
    MsgBox(0, "STDERR read:", $line)
Wend