Step 1: Pat the beef short ribs dry with paper towels. Season generously with 1 tsp salt and 1/2 tsp black pepper on all sides.
Step 2: In a large Dutch oven or heavy-bottomed pot, heat the cooking oil over medium-high heat. Sear the beef short ribs in batches until deeply browned on all sides, about 3-4 minutes per side. Remove the seared ribs and set aside.
Step 3: Reduce the heat to medium. Add the minced garlic and sliced onion to the pot. Sauté for 3-5 minutes until the onion softens and becomes translucent, and the garlic is fragrant, being careful not to burn it.
Step 4: Deglaze the pot by pouring in the vinegar. Scrape up any browned bits from the bottom of the pot with a wooden spoon. Let the vinegar simmer for 1-2 minutes until its strong acidic aroma cooks off slightly.
Step 5: Stir in the soy sauce, water (or beef broth for extra flavor), bay leaves, and whole black peppercorns. Bring the mixture to a gentle simmer.
Step 6: Return the seared beef short ribs to the pot, ensuring they are mostly submerged in the liquid. If not, add a little more water or broth until they are. Bring to a boil, then reduce the heat to low, cover the pot tightly, and let it simmer for 2.5 to 3 hours, or until the beef is fork-tender. Check periodically to ensure liquid levels are adequate.
Step 7: Once the beef is tender, remove the lid. Skim off any excess fat from the surface of the sauce if desired. Increase the heat to medium and simmer uncovered for another 20-30 minutes, or until the sauce has thickened to your desired consistency. The sauce should reduce and become richer.
Step 8: Taste the sauce and adjust seasoning if necessary. You might want a pinch of sugar to balance the flavors, or a bit more soy sauce for saltiness. Remove the bay leaves before serving.
Step 9: Serve the Filipino Beef Short Ribs Adobo hot over freshly steamed white rice, garnishing with chopped green onions if desired.