Mix tomatoes, onions, apple cider vinegar, green bell peppers, seeded chopped chile peppers, sugar, unseeded chopped chile pepper, salt, allspice, cinnamon, and cloves together in a large mixing bowl.
Ladle enough of the tomato mixture into the pitcher of a blender to fill to about 3/4-full; blend until smooth. Pour blended mixture into a large pot. Repeat blending until entire mixture has been pureed.
Bring the mixture to a boil, reduce heat to medium-low, and simmer until thickened, 7 to 8 hours.