Start by seasoning the beef cubes with salt and pepper, then sprinkle the flour over them. Toss to coat evenly.
In a large skillet over medium-high heat, heat the olive oil. Once hot, add the beef in batches, browning on all sides. This should take about 5-7 minutes per batch. Transfer the browned beef to the slow cooker.
In the same skillet, add the pearl onions and mushrooms. Sauté for about 4-5 minutes until they start to soften. Add the minced garlic and cook for an additional minute until fragrant. Transfer this mixture to the slow cooker.
Pour the red wine into the skillet to deglaze, scraping up any browned bits from the bottom. Let it simmer for a minute, then add the beef broth, tomato paste, thyme, and bay leaf. Stir well to combine.
Pour the wine mixture over the beef and vegetables in the slow cooker. Stir gently to mix everything together.
Cover and cook on low for 7-8 hours or on high for 4-5 hours, until the beef is tender and the flavors are well combined.
Once cooked, taste and adjust the seasoning with more salt and pepper if needed. Remove the bay leaf before serving.
Serve hot, garnished with fresh parsley.