Place the boneless skinless chicken thighs in a mixing bowl, ensuring they are in a single layer for even marination.

Add the red onion, olive oil, chipotle pepper, adobo sauce, minced garlic, cumin, oregano, and ancho chili powder to the bowl. Toss everything thoroughly.

Cover the bowl with plastic wrap and marinate in the refrigerator for at least 4 hours, preferably overnight.

Preheat the oven to 400°F (200°C). Spread the marinated chicken on a lined baking sheet.

Bake for 20-30 minutes until cooked through, reaching an internal temperature of 165°F (75°C). Broil for 1-2 minutes for added texture.