Pre-heat oven to 170C/325F/Gas 3.
Heat a large Dutch oven or casserole dish (with lid) over medium heat. Add bacon and cook for 4-5 minutes, stirring occasionally, until crispy. 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 the Dutch oven.
Add the beef pieces and season with salt and black pepper, to taste. Cook for 4-5 minutes, stirring occasionally until browned on all sides. Remove beef and transfer to the same plate with the bacon. Set aside.
Add red onion, pearl onions, carrots, and garlic. Cook for 4-5 minutes, stirring occasionally until the veggies become fragrant and translucent.
Add the 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 the heat to medium-high and bring to a gentle boil, stirring occasionally.
Remove from heat, cover, and transfer the Dutch oven into the center of the preheated oven.
Cook for 2½ to 3 hours, stirring every 40-50 minutes.
Remove from the oven and discard the bay leaves and thyme sprigs.
To prepare in the slow cooker: Dredge the beef in the flour (you can use regular flour if you wish) and cook the bacon and beef as above. Transfer to the slow cooker pot. Add the red onion, pearl onions, carrots, garlic, and mushrooms to the pot. Add tomato paste, and half-measurement of the red wine and beef broth. Add the bay leaves and thyme. Cook on high for 4-6 hours, or low for 8-12 hours.
Serve immediately topped with fresh chopped parsley, if desired. Enjoy!