Trim excess skin from chicken thighs and legs. Dredge chicken in flour seasoned with salt and pepper.
Brown bacon in a large pan, then remove and set aside. Brown chicken pieces in bacon fat in batches.
Sauté carrot, celery, onion, and garlic in the same pan. Add tomato paste, chicken stock, red wine, thyme, and bay leaves. Bring to a boil, scraping up browned bits.
Return chicken and bacon to the pan. Cover and braise in a 350°F oven for 90 minutes.
Sauté mushrooms and pearl onions in butter and olive oil until browned. Season with salt, pepper, and thyme.
Remove chicken from the pan. Reduce the sauce on the stovetop until thickened. Add dark chocolate for richness.
Serve chicken with sauce, mushrooms, onions, and garnish with parsley. Adjust seasoning as needed.
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