Place top oven rack in the center position and pre-heat oven to 325°F.
Heat a large Dutch oven over medium heat. Add bacon and cook, stirring occasionally, until crispy, approximately 4-5 minutes. Transfer bacon to a plate lined with paper towels and blot off excess grease. Set aside.
Drain and discard all but 1 tablespoon bacon grease from Dutch oven. Add beef chunks and season with salt and black pepper, to taste. Cook, stirring occasionally, until browned on all sides, approximately 4-5 minutes. Remove beef and transfer to the same plate with the bacon. Set aside.
Add red onion, pearl onions, carrots, and garlic. Cook, stirring occasionally, until the veggies become fragrant and translucent, approximately 4-5 minutes.
Add mushrooms and sprinkle with almond flour. Cook, stirring frequently, for 1-2 minutes or until the mixture starts to thicken.
Return bacon and beef to the Dutch oven. Add tomato paste, red wine, beef broth, bay leaves, and fresh thyme. Season with additional salt and black pepper, to taste, and stir to combine.
Increase heat to medium-high and bring to a gentle boil, stirring occasionally. Remove from heat, cover, and transfer Dutch oven into the pre-heated oven. Cook for 2½ to 3 hours, stirring every 40-50 minutes.
Remove from oven and discard bay leaves and thyme sprigs. Serve immediately topped with fresh chopped parsley, if desired. Enjoy!