Zinc (Zn) biofortification breeding lines show different grain Zn contents in various environments and in response to Zn fertilizer application, but it is not clear which environmental variables are most important in explaining this.  An experiment was conducted in four contrasting sites in the Philippines: IRRI (Zn-depleted, pH 6.6), Bay (low Zn, high organic matter, pH 6.3), Nueva Ecija (Zn-sufficient, pH 4.5) and Bukidnon (continuously submerged, high iron content, pH 4.8). Twenty-one genotypes were grown on each site with three replicates; the Zn fertilizer treatments were no added Zn and 10 kg Zn ha^-1 as zinc sulfate, applied at panicle initiation. Water management status was monitored, and grain yield and grain Zn concentration were analyzed. The data show that the IRRI site had the highest average grain yield (7 t ha^-1) compared with the other sites. Popular varieties such as IR64 and PSBRc 82 produced 4–7 t ha^-1, whereas local check variety NSIC 158 produced 5–8 t ha^-1. Grain Zn concentration was significantly higher in the Zn-fertilized plots at Nueva Ecija, IRRI, and Bay. IR69428, IR68144, and IR91152 were the three genotypes with the highest grain Zn on the four sites. A negative correlation was found between grain yield and grain Zn concentration. This study provides plant breeders some understanding of how Zn biofortification breeding lines perform in different environments, in terms of grain yield and grain Zn concentration. This helps them identify which environmental factors cause variation in grain Zn concentration.