Prebiotic effects have been attributed to agave fructans through bacterial and yeast fermentations, but there are few reports on their use as raw materials of a carbon source. Kefir milk is a fermented drink with lactic acid bacteria and yeast that coexist in a symbiotic association. During fermentation, these microorganisms mainly consume lactose and produce a polymeric matrix called kefiran, which is an exopolysaccharide composed mainly of water-soluble glucogalactan, suitable for the development of bio-degradable films. Using the biomass of microorganisms and proteins together can be a sustainable and innovative source of biopolymers. In this investigation, the effects of lactose-free milk as a culture medium and the addition of other carbon sources (dextrose, fructose, galactose, lactose, inulin and fructans) in concentrations of 2, 4 and 6%w/w, coupled with initial parameters such as temperature (20, 25 and 30 °C), % of starter inoculum (2, 5 and 10%w/w) was evaluated. The method of response surface analysis was performed to determine the optimum biomass production conditions at the start of the experiment. The response surface method showed that a 2% inoculum and a temperature of 25 °C were the best parameters for fermentation. The addition of 6%w/wagave fructans in the culture medium favored the growth of biomass (75.94%) with respect to the lactose-free culture medium. An increase in fat (3.76%), ash (5.57%) and protein (7.12%) content was observed when adding agave fructans. There was an important change in the diversity of microorganisms with an absence of lactose. These compounds have the potential to be used as a carbon source in a medium culture to increase kefir granule biomass. There was an important change in the diversity of microorganisms with an absence of lactose, where the applied image digital analysis led to the identification of the morphological changes in the kefir granules through modification of the profile of such microorganisms.