Not to my knowledge. Smokeboost has to be activated from the app or controller and deactivated the same way. I have never used the cook programs but I don't think a program would do that either. However, I can't say I know that from experience so it's my best guess. There are 2 schools of thought on using Smokeboost for long cooks. The first is that it adds more smoke flavor and they don't mind the extra time on the cook. The second is that the Smokefire puts out so much smoke flavor that smokeboost is not needed on long cooks. However you do it, have fun.