The effect of three altitudes (1570, 1720 and 1890 masl) on fruit quality of four guava genotypes (Regional Roja, RR; Regional Blanca, RB; Guavata Victoria, GV; Raquira Blanca, RQ) growing in a traditional semi-wild crop system was studied. Fruit weight and colour development were affected by the environment. At lower altitudes, where warmer temperatures and high radiation predominate, a higher fruit weight was accompanied by quick colour change from green to yellow in RR and GV, while the opposite trend occurred at the highest altitude, but this response was not observed in RB or RQ. A significant genotype × environment interaction was found for fructose, sucrose and organic acid content (malic, citric, succinic, oxalic and ascorbic acids). In general, organic acid content increased with altitude with the exception of one genotype. Environmental factors associated with altitude that affected the differences in fruit quality among the genotypes were vapour pressure deficit (VPD), maximum photosynthetic photon flux density (PPFDmax) and temperature difference between day and night (∆T°). The differences in organic acid content can be a good tool to provide guava fruit with different tastes to the market, according to consumer preferences, and for quality-oriented breeding with selected growing areas to produce extra-quality fruit.