If you are using precooked or canned beets, skip this step.
Otherwise, add the fresh beets to a medium saucepan and cover with 3 cups water. Bring to a boil over medium- high heat, then reduce the heat to a simmer and cook for about 25 minutes, or until tender. Drain and rinse under cold water until cool enough to handle. Reserve the saucepan.
In a blender (preferably high-powered), combine the beets, ketchup, vinegar, liquid aminos, mustard powder, smoked paprika, onion powder, garlic powder, salt, and pepper and blend on low speed for 1 to 2 minutes. Then blend on high speed for about 30 seconds more, or until smooth.
Transfer the mixture to the now-empty saucepan. Set over medium-low heat and cook, whisking now and then, for 5 to 7 minutes, until the sauce thickens.
Use immediately or cool completely before storing in an airtight container in the refrigerator for up to 2 weeks.