Use a coarse hand or box grater to shred the peeled beets.
Add them to a large pot with the onion, apple, ginger, salt, sugar, apple cider vinegar, and water. Cover and bring to a boil, then reduce heat to low and let the relish cook for ~30 minutes. Take off the lid and simmer for another 10-15 minutes to let some of the excess water evaporate.
Remove from heat and carefully pour out any liquid that's still left in the pot. Taste and adjust seasonings as desired. Transfer to glass jars or airtight containers, and enjoy!
Store in the fridge for 1-2 weeks or in airtight containers in the freezer for up to 3 months.
Serve on sandwiches, burgers, taco, fish, toast, yogurt, oatmeal, or charcuterie boards.