Rinse the mustard seeds with water through a sieve or through a cheese cloth.
Add the rinsed seeds, ¾ cup of the apple cider vinegar, and salt to a small bowl and soak for two hours at room temperature.
Add the soaked mustard seeds to a small pot. Stir in the honey or sugar, red pepper flakes and black pepper. Bring to a quick boil, then reduce the heat and simmer for 20 minutes.
Allow to cool. Stir in the remaining ¼ cup vinegar and transfer to a sealable jar or container. Keep in the refrigerator.
