Add cherries and honey to a small pan and bring to a boil over medium-high heat. Lower heat to a simmer and continue cooking until cherries have softened, about 5 minutes. Set aside to cool.
Whisk protein powder and dutch cocoa into almond milk until smooth. Mix in oats and chia seeds, then layer half of the mixture into the bottom of a jar or resealable container.
Add yogurt on top of oats, then add cherries on top. Finish with the rest of the oat mixture. Cover and refrigerate overnight.