Cut onions into very thin slices; place in two 1-quart glass jars or one large bowl, packing them tightly together. Add garlic cloves, jalapeno slices, bay leaves, and pepper flakes.

Combine vinegar, water, sugar, salt, and peppercorns in a medium saucepan over medium-high heat. Bring to a simmer. Cook, stirring often until sugar and salt dissolve. Remove from the heat and let stand for 10 minutes.

Pour warm liquid over the onions and press down if necessary to submerge. Cover and refrigerate, 8 hours to overnight. Serve immediately or store in the refrigerator for up to 1 month.