Start by seasoning the chicken thighs with salt and pepper.
Heat the olive oil in a 5 ½ - 6-quart or pot over medium-high heat; cook the chicken thighs in batches once the oil is hot.
Cook the chicken thighs for 3-4 minutes on each side. You’re just browning the chicken; it will finish cooking in the sauce. Place the cooked chicken in a bowl while you cook the other ingredients.
In the same pot, add another tablespoon of olive oil. Over medium heat, saute the onions until soft and transparent, about 3-4 minutes.
Add in the garlic and cook for another 30 seconds or so.
Then, add in the peppers and mushrooms and cook until soft. Stir in the thyme and cook for another 30 seconds.
Pour in the red wine and let it cook for 2-3 minutes or reduced. While the wine is simmering, scrape the brown bits from the bottom of the pot. You’ll get a lot of flavor in those bits!
Add the crushed tomatoes and tomato sauce.
Give the sauce a few stirs, and return the chicken to the sauce.
Add the bay leaves.
Bring to a boil and then immediately reduce the heat to a simmer, stirring occasionally. Let the sauce simmer on low for an hour. The chicken should be tender, moist, and falling apart, and the sauce should be a deep red color. With a large spoon break the chicken into chunks after it cooks.
Remove and discard the bay leaves.
If needed, season with salt, then serve hot over gluten-free pasta or your favorite side.
If the sauce becomes too thick, add a splash of chicken broth and stir.