Place the peppers, cut side down in a microwave-safe baking dish. Add 1 cup water to the baking dish. Cover. Microwave on high until the peppers are just starting to soften, 4 to 5 minutes. Carefully remove cover, drain off water.
Heat oil in skillet. Add beef and cook, crumbling with a wooden spoon until the meat is browned. Add onion and mushrooms and cook, stirring often, until the vegetables are softened.
Stir in cumin, chili powder, chipotle, salt and cinnamon and cook until fragrant, about 30 seconds.
Remove from heat and stir in tomato puree.
Fill the peppers with the meat mixture (about ½ cup per pepper half).
Top with cheese. Microwave the peppers in the baking dish, uncovered until the cheese is melted and the peppers are tender, 2 to 3 minutes. Serve warm with cilantro on top if desired.