Fungus-farming termites (Macrotermitinae) engage in an obligate mutualism with members of the fungal genus Termitomyces, which they maintain as a monoculture on specialized comb structures. Both these comb structures and the guts of the termites host diverse bacterial communities that are believed to assist in sustaining monoculture farming through antagonist suppression. Among candidate bacteria-derived compounds serving this function are non-ribosomal peptides (NRPs), which are a highly bioactive class of specialized metabolites, frequently produced by symbionts within eukaryotic hosts. However, our understanding of specialized metabolites in termite-associated microbiomes is limited. Here we use amplicon sequencing to characterize both bacterial composition and NRP potential. We show that bacterial and NRP diversity are correlated and that the former varies more than the latter across termite host and gut and comb samples. Compositions of the two are governed by host species and sample type, with topological similarity indicating a diverse set of biosynthetic potential that is consistent with the long evolutionary history of the Macrotermitinae. The structure of both bacterial and NRP compositional networks varied similarly between guts and combs across the Macrotermitinae albeit with auxiliary termite genus-specific patterns. We observed minimal termite species-specific cores, with essentially no Macrotermitinae-wide core and an abundance of putatively novel biosynthetic gene clusters, suggesting that there is likely no single solution to antagonist suppression via specialized NRP metabolites. Our findings contribute to an improved understanding of the distribution of NRP potential in the farming termite symbiosis and will help guide targeted exploration of specialized metabolite production.