As truffle cultivation expands, growers empirically develop new agronomic management practices aimed at promoting truffle growth such as “truffle nests”, localized peat amendments that are supplemented with truffle spore inoculum. Previous research showed that nests contain lower fungal diversity than the surrounding soil, which could encourage its occupation by pioneer species such as Tuber melanosporum. However, truffle nests did not quickly stimulate truffle mycelium growth. We hypothesized that the bacterial community from the soil may be the first to colonize nests and that fungal and bacterial diversity in nests would have an inverse relationship. To test this, we characterized the bacterial community of truffle nests, via 16S rRNA gene amplicon sequencing, in two orchards during the two years after establishing the nests. Unexpectedly, we did not find drastic differences in the bacterial diversity inside nests with respect to the bulk soil or the commercial substrate before being introduced in the field. However, Proteobacteria richness in nests was positively correlated to truffle mycelium abundance, which together with a higher relative abundance of Proteobacteria in nests than in bulk soil, indicates a possible underlying factor for the performance of nests in truffle plantations. Fungal and bacterial richness was positively correlated in nests, countering our hypothesis that bacterial diversity would negatively impact fungal diversity.