Heat the olive oil in a large skillet over medium-high heat. Add the beef pieces in a single layer and sear until browned on all sides, about 5 minutes total. Transfer the beef to the slow cooker.
Add the sliced onions to the same skillet and cook for 4 minutes until they begin to soften. Stir in the garlic and cook 30 seconds more.
Sprinkle the flour over the onions and stir to coat. Pour in the balsamic vinegar and beef broth, scraping the bottom of the skillet to release any browned bits.
Transfer the onion mixture to the slow cooker. Add the mushrooms, thyme, salt, and pepper. Stir everything to combine.
Cover and cook on low for 7 to 8 hours until the beef is very tender and the broth has thickened slightly.
Taste and adjust salt or pepper if needed before serving.