Pat the chicken dry and season with 3 teaspoons kosher salt and 1½ teaspoons black pepper. Pour the red wine on top. Add the thyme sprigs, shallots, and bay leaves. Mix to coat the chicken with the wine. Cover and transfer to the refrigerator for 4 to 24 hours.
Prepare the onions:
Bring a medium pot of water to a boil. Once boiling, add the pearl onions and boil for 5 minutes. Use a slotted spoon to transfer them to an ice bath. Let stand in the ice water for 5 minutes.
Using kitchen shears, snip off the bottom of the onion. Squeeze from the top to remove the onion from its skin. Continue until you finish peeling all the onions. Discard the skins.
Prep the chicken:
Remove the chicken from the refrigerator. Transfer the chicken to a paper towel-lined plate. Pat the chicken dry and set aside. Fish out and remove the bay leaves, thyme sprigs, and shallots from the wine. Reserve the wine and discard the spent aromatics.
Cook the bacon:
Place the sliced bacon in a large, heavy-bottomed pot. Turn the heat to medium and cook, turning regularly, for 5 to 7 minutes, until browned and crispy. Transfer the bacon to a bowl with a slotted spoon, leaving the rendered fat in the pot.
Brown the chicken:
Turn the heat on the bacon fat to medium. Add the chicken, skin-side down, and cook without moving for 5 minutes until browned. Flip and cook for 3 minutes. Transfer to a plate.
Drain off and discard all but 1 tablespoon of fat from the pot.
Cook the vegetables:
Add the diced onion, carrots, parsnips, and mushrooms to the pot. Season with ½ teaspoon kosher salt and ½ teaspoon black pepper. Cook, turning regularly, for 8 to 12 minutes until the mushrooms deepen in color and the carrots and parsnips soften.
Add the minced garlic and tomato paste and stir to coat the vegetables in tomato paste. Add the flour and cook for 1 to 2 minutes.
Deglaze the pot:
Pour the brandy into the pot. Bring to a boil for 3 minutes.
Add the reserved wine from the marinade and 1 cup chicken broth. Bring to a boil, stirring to create a smooth sauce. Reduce the heat to low.
Simmer the coq au vin:
Add the cooked bacon and pearl onions. Arrange the chicken thighs, skin-side up, on top of the broth. Cover and simmer for 1 hour.
Remove the lid and simmer uncovered for 15 to 20 minutes until the broth thickens further. Taste and add more salt and pepper if needed. Turn off the heat.
Sprinkle half the minced parsley over the chicken and let stand for 5 minutes.
To serve:
Serve the chicken and vegetables with roasted or mashed potatoes, sprinkling the remaining fresh parsley over each plate. Enjoy!
Notes
Note 1: If you use frozen pearl onions, you can add them straight to the sauce later in the recipe. If you use fresh pearl onions, follow the instructions in the recipe to peel them.