Numerous fruits are produced in Ecuador, of which about 40% are never eaten. In addition, fresh goat cheeses are in high demand. However, goat cheese generates goat milk whey with high contamination loads, and, therefore, it must be adequately treated before being discharged into ecosystems. This research aims to use a mixture of tree tomato, common strawberry juices, and goat’s milk whey, to be statically fermented by milk and water kefir grains (WKG) for 48 h. For this, a dual mixture design of L-optimal response surface methodology was carried out to find the conditions that maximized all the responses evaluated (lactic-acid bacteria and yeasts concentrations and the overall acceptability assessed on a 7-point scale). Experiments were carried out in San Gabriel, Ecuador. Temperatures during the day and night were 20.2 ± 0.3 °C and 18.7 ± 0.3 °C, respectively. Three conditions were selected, where the highest response values were reached. Complementary experiments demonstrated the validity of the models. When comparing the results of the present study with similar ones carried out previously, higher values were observed in the concentration of yeasts, which seems related to the presence of the WKG. It is concluded that they could be suitable functional beverage candidates.