In a large mixing bowl, whisk together the olive oil, fresh orange juice, lime juice, minced garlic, ground cumin, dried oregano, salt, black pepper, and red pepper flakes to prepare the mojo marinade.
Add the chicken thighs to the bowl, coating each thoroughly with the marinade. Cover and refrigerate for at least 30 minutes, preferably an hour or longer.
Heat a large skillet over medium-high heat. Add chicken thighs skin-side down and cook until the skin is golden brown and crispy, about 5-7 minutes. Flip and brown the other side for 3-4 minutes. Remove chicken and set aside, keeping pan juices.
In the same skillet, sauté the diced onion and bell pepper until softened and fragrant, about 4-5 minutes, scraping up browned bits for extra flavor.
Add the yellow rice to the skillet, stirring it into the vegetables and toasting slightly for 1-2 minutes. Pour in the chicken broth and stir to combine.
Return the browned chicken thighs to the pan, skin-side up. Cover with a lid, reduce heat to low, and simmer for 25-30 minutes until rice is tender and chicken is cooked through.
Sprinkle fresh chopped cilantro over the dish before serving for a bright, fresh finish.