Trim the stems from the mushrooms and use a spoon to scrape out the gills. Set mushrooms aside.
Coat a large nonstick pan with cooking spray and add the onions and thyme. Place the pan over medium heat, cover, and cook for several minutes, until the onions are tender. Add little water during cooking if the skillet becomes too dry.
Add the spinach and garlic and saute for a minute or two until the spinach is wilted. Remove the skillet from the heat and stir in the tomatoes, couscous, and cheese.
Place 1/4 of the mixture in the depression in each mushroom cap, mounding the top slightly. Spray the tops lightly with cooking spray. Place the stuffed mushrooms on a large baking sheet and bake, uncovered, for 15 minutes, until the mushrooms have become tender and the topping is lightly browned. Serve hot.