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Heat 2 tablespoons olive oil in a large high-sided skillet or Dutch oven over medium heat. Add chicken thighs and sear on all sides until a golden crust forms, 4-5 minutes. Season generously with salt and pepper on all sides.
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Remove the chicken thighs from the skillet and set aside on a plate.
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In the same skillet, add onions and mushrooms and season to taste with salt and pepper. If necessary, add an additional 1 tablespoon of olive oil.
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Cook until the onions become translucent, and the mushrooms soften, approximately 4-5 minutes.
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Add garlic and bell pepper and continue cooking for another 2-3 minutes.
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Add wine, crushed tomatoes with their juices, oregano, red pepper flakes, olives, and capers. Stir to combine.
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Bring the sauce to a gentle simmer over medium-low heat.
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Add the chicken and any accumulated juices back to the sauce and cook until the chicken is cooked through and the sauce is slightly thickened, approximately 30-35 minutes.
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Remove from heat and stir in the fresh parsley. Taste and adjust the seasoning as desired. Serve over cooked spaghetti or polenta.