The disposal of whey, the main by-product of the cheese industry, represents a challenge as it is a significant pollutant due to its complex composition. In Mexico, whey is used to produce Requesón, a type of protein-rich whey cheese that generates another by-product, secondary whey. This residue has a lower protein content but still retains the lactose of primary whey, which means it still represents an environmental hazard. Therefore, simple and economical solutions are needed. In the present study, secondary whey was used as a fermenting substrate for kefir grains to produce functional bioproducts such as exopolysaccharides (EPSs) like kefiran. The secondary whey was pasteurized at 121 °C for 10 min before its inoculation with 10% (w/v) kefir grains and then incubated at 30 °C for 24 h. After the removal of kefir grains by filtration, the fermented whey was heated in a boiling water bath for 15 min and then centrifuged. The supernatant was adjusted to pH 7.0, and the EPSs were precipitated by the addition of two volumes of absolute ethanol and then kept at 4 °C for 24 h. The precipitate was separated by centrifugation, resuspended in deionized water, dialyzed for 24 hours using a 10 kDa pore-sized membrane and finally lyophilized. The phenol–sulfuric acid method was used to determine total carbohydrates and the Bradford method was used for protein content. The isolated solid had a composition of 57.96 ± 0.34 µg of carbohydrates/mg and 36.62 ± 0.59 µg of protein/mg. Hence, secondary whey fermentation with kefir grains is a suitable solution to reduce the environmental impact of whey and to produce functional bioproducts like EPSs.