Did the Prophet ﷺ use the miswak when he woke up?

Short answer

Whenever the Prophet ﷺ got up at night, he would clean his mouth with the miswak. Keep a miswak (or your toothbrush) beside your bed. Use it before you check anything. It is Day 7 of the 30-Day Sunnah Habit Planner, a habit that takes under a minute.