Step 1- Soak and cook the lentils. Rinse the lentils thoroughly under running water for about 1 minute, then let them soak in a small bowl for 10 minutes. Bring 2 cups of water to a boil, add the lentils, and cook for 10-15 minutes until al dente. Older lentils may need a few extra minutes, so keep an eye on them. Drain and rinse with cold water to stop the cooking process.
Step 2- Prep the zucchini and preheat the oven. Position a rack in the center of the oven and preheat to 400°F. Spray a 9x13 baking dish with cooking spray. Using a small spoon, scoop out the center of each zucchini half, leaving a ¼-inch border on all sides. Line the zucchini in the baking dish, skin side down, and set aside.
Step 3- Cook the filling. Heat the olive oil in a skillet over medium-high heat. Add the diced onions and cook for 3-4 minutes until they start to brown, then add the garlic and cook for another 30 seconds. Stir in the baby spinach and cooked lentils, letting the spinach just begin to wilt. Add the pasta sauce and let everything heat through for 1-2 minutes. Stir in the red pepper flakes, then taste and adjust seasoning as needed.
Step 4- Stuff and bake. Divide the lentil mixture evenly among the prepared zucchini boats. Top each one generously with shredded vegan mozzarella. Cover the baking dish with foil and bake for 30-35 minutes. For a bubbly, golden cheese finish, remove the foil during the last 2 minutes and switch on the broiler.