The dynamics of adaptive response to abiotic environmental factors is well documented in a variety of systems, but the role of biotic environment in the adaptive process is less well understood. Ubiquitous microbial communities associated with hosts can be commensal, but some microbiota result in pathogenic infection that challenges the host with consequences ranging from resource reallocation away from other functions to rapid host lethality. The immune system sits at the crucial interface between an organism’s external and internal environment and this balance between self and other may be essential in adaptation to environmental heterogeneity. Therefore, immune response may be an important trait to respond to biotic variation along environmental gradients. Here, we investigate innate immunity along spatial and temporal environmental gradients in wild populations of Drosophila melanogaster. We find a repeated complete seasonal turnover in the microbial environment associated with wild flies from spring to fall and a corresponding change in the immune response. We simultaneously sampled populations along a latitudinal cline early and late in the season and evaluated the response to infection. Both gram+ (Enterococcus faecalis) and gram- (Providencia rettgeri) bacteria were used to probe both Toll and IMD immune pathways that are initiated by different pathogen challenges. We find opposing seasonal responses to the gram+ and gram- pathogens, suggesting a seasonal trade-off in defense that is consistent with the frequency dependent selection imposed by the seasonally changes in the bacterial composition in these populations. Whole genome resequencing in these populations identified alleles in immune genes that cycle across seasonal time. We evaluate the function of natural polymorphisms within Thioester-containing protein 3 (Tep3) and among other immune genes and demonstrate non-additive interactions among alleles that contributes to the seasonal differences in immune response in natural populations; these non-additive interactions shape the frequency of the genotypes in the wild across seasonal time. Overall, the data demonstrate that the innate immune response in wild Drosophila has a genetic basis that varies with location, season, and pathogen; the trade-offs among innate immunity and other life history traits predict that the biotic environment may be an important underlying selective force in wild populations.