Heat oven to 375°F. Spray 12 regular-size muffin cups with cooking spray.
Cook Brussels sprouts for the minimum time as directed on box; pour into medium bowl. Cool 5 minutes. Cut Brussels sprouts in half. Stir in mushrooms, thyme and pepper.
In medium bowl, stir Bisquick mix, milk and eggs with whisk or fork until blended. Spoon slightly less than 1 tablespoon batter into each muffin cup. Divide Brussels sprouts mixture evenly among cups; sprinkle each with about 1 tablespoon cheese. Top each with 1 tablespoon batter.
Bake 22 to 27 minutes or until toothpick inserted in center comes out clean and tops are golden brown. Cool 5 minutes. With thin knife, loosen sides of pies from pan; remove from pan to cooling rack. Serve warm.