Bring a large pot of salted water to a boil. Add the beets and blanch until the skin becomes loose, 5 to 10 minutes. Shock the beets in ice water to cool.
Combine 6 cups water, 1/4 cup salt, the onion, sugar, bay leaves, thyme sprigs, orange zest, orange juice, allspice, mustard seeds, canela, cloves, rice wine vinegar, balsamic vinegar and honey in a separate pot; stir to incorporate and bring to a simmer.
Peel the skin from the beets and halve or quarter if large. Divide among jars. Pour the pickling liquid over and allow to cool at room temperature. Refrigerate up to 2 weeks.