Mexico is among the most important citrus fruit producers in the world. However, during storage, several problems related to fungi can arise. The most common fungal postharvest diseases detected on Citrus limon var Eureka (Italian lime) produced in the Tamaulipas state are green/blue mold (Penicillium spp.), fusarium rot (F. oxysporum, F. solani, F. proliferatum, among others), and anthracnose (Colletotrichum spp.). In this work, we selected yeasts, occurring as the natural epiphytic mycoflora of lemons or from fermented traditional products, to be tested as part of a formulation for protecting stored lemons against fungal diseases. The best-performing yeasts, labeled as LCBG-03 (Meyerozyma guilliermondii), LCBG-30 (Pseudozyma sp.), and LCBG-49 (Saccharomyces cerevisiae), were selected to test their compatibility and biocontrol performance against strains of Penicillium digitatum (AL-38), Fusarium sp. (AL-21), Colletotrichum gloeosporioides (AL-13), and Epicoccum sorghinum (H3A). Based on their in vitro performance regarding the percentage of radial growth inhibition, both applied individually or as two yeasts mixed at equal cellular concentrations, the best combinations (containing M. guilliermondii formulated with either Pseudozyma sp. or S. cerevisiae) were selected with efficacies higher than 95% in both in vitro fungal radial growth rate inhibition and on stored lemon fruits. This work contributes to the search for compatible yeast combinations with the aim to diminish the fungal losses of citrus fruits using biocontrol for citrus postharvest protection.