Preheat the oven to 400°F (200°C).
Cut the spaghetti squash in half lengthwise and scoop out the seeds.
Place the squash halves cut-side down on a baking sheet lined with parchment paper.
Bake for 35-40 minutes, or until the squash is tender and strands easily separate with a fork.
While the squash is baking, heat olive oil in a large skillet over medium heat.
Add the diced chicken to the skillet and season with cumin, chili powder, smoked paprika, garlic powder, onion powder, salt, and black pepper.
Cook the chicken for 6-8 minutes, stirring occasionally, until fully cooked and lightly browned.
Remove the skillet from heat and stir in the diced tomatoes, black beans, corn, green bell pepper, red bell pepper, and cilantro.
When the spaghetti squash is cool enough to handle, use a fork to scrape out the strands into a large mixing bowl, discarding the squash skin.
Add the cooked chicken mixture to the bowl with the spaghetti squash and mix until well combined.
Transfer the mixture to a greased 9×9-inch casserole dish and spread evenly.
Sprinkle the shredded Mexican blend cheese and cheddar cheese evenly over the top.
Bake the casserole in the oven at 375°F (190°C) for 10-15 minutes, or until the cheese is melted and bubbly.
Remove from the oven and let cool for 5 minutes.
Garnish with chopped green onions and serve with a dollop of plain nonfat Greek yogurt.