Pierce the shell of the spaghetti squash with a fork and place in a microwave-safe dish; cook in microwave on High for 12 minutes. Set aside to cook until cool enough to handle. Slice in half lengthwise; remove the seeds. Use a fork to pull the flesh of the squash away from the shell and place into a large bowl; fluff with the fork to separate the strands as much as possible.
Heat the olive oil in a large skillet over medium heat. Cook and stir the onion in the hot oil until just tender, about 3 minutes. Add the garlic and continue cooking and stirring another 3 minutes. Stir the zucchini and green bell pepper into the mixture; season with the Italian herb seasoning and black pepper. Pour the tomatoes into the skillet. Continue cooking just until the tomatoes are warmed, 3 to 5 minutes. Add the squash to the skillet and toss until evenly mixed. Sprinkle with the feta cheese and toss again to serve.