Aerobic Bacillus bacteria, yeasts, and micrococci are pigment-forming microorganisms responsible for color defects in cheese production. The article describes their environment, industry-related characteristics, types of defects they cause, and various color violations in commercial cheeses. The research featured domestic cheeses with yellow and red surface spots that appeared during industrial ripening and storage. Pigment-forming microorganisms developed on cheese surface at a low ripening temperature, high concentration of table salt, and critically low oxygen. Pigment-forming microflora proved to enter cheese from milk, brine, or production environment, e.g., water, air, and processing equipment, dry and succulent feeds being the main source of milk contamination with spore-forming aerobic bacteria, yeast, mold fungi, etc. Contamination of raw milk, milking equipment, and air environment with micrococci was primarily associated with cows’ udder and skin. Cheese production presupposes low-temperature heat treatment of raw milk, which means possible residual microflora in pasteurized milk. As a result, the total count of mesophilic aerobic and optionally anaerobic microorganisms, i.e., the potential pigment formers, was to stay below 104 CFU/cm3. Yeast and spore-forming Bacillus microorganisms demonstrated the acceptable level of ≤102 CFU/cm3 in milk intended for cheesemaking. If their total count exceeded 103 CFU/cm3, it indicated high microbiological risks of cheese appearance defects. The microflora responsible for discoloration of cheese surface was represented by yeast, micrococci, aerobic spores, or their combinations.