Stab several holes in the potato with a fork. Heat in a microwave oven on high setting until tender, about 5 minutes. Remove when cool enough to handle.
Cut potato in half; scoop out the flesh, leaving skin intact. Place flesh in a bowl; reserve skins. Add vegan cheese, chives, imitation bacon bits, vegan sour cream, salt, and pepper; mix filling together.
Spoon filling back into the potato skins and place on a microwave-safe plate. Cook in the microwave oven on high setting until filling is heated through, about 2 minutes.