Preheat oven to 350 degrees. Cook pasta according to package directions, drain.

Meanwhile, heat olive oil to medium in a large Dutch oven. Add onion, green pepper, red pepper and jalapeño. Cook for 10 to 12 minutes, until tender. Add garlic and cook for 1 minute. Add tomato paste, cumin, chili powder and paprika and stir until well combined.

Sprinkle in flour slowly and whisk until blended. Gradually add in milk. Bring to a simmer and cook for 4 to 5 minutes. Add tomatoes and one cup of cheese and stir until cheese melts. Remove from heat and stir in pasta and chicken or tempeh. Transfer to baking dish and top with remaining cheese. Cook for 30 minutes, until bubbly. Garnish with cilantro and served.