Plant domestication studies have traditionally focused on morphological factors that are under direct selection, e.g., fruit size, overlooking the consequences of domestication on ecosystem services. We addressed this knowledge gap by documenting for first time the soil carbon (C) sequestration potential in wild relatives and domesticated cultivars of breadfruit (Artocarpus), a long-lived tree crop. We evaluated aggregate-bound and bulk organic C pools in breadfruit wild relatives and domesticates in soils that varied in nitrogen (N) and phosphorus (P) fertility with management practices (fertilizer and mulch). We determined whether C levels were linked to plant domestication, abiotic factors (N, P, pH, and texture), or biotic factors with known links to C accrual (arbuscular mycorrhizal fungi (AMF), and microbial biomass). In low N or N: P soils, increasing breadfruit domestication was associated with reductions in macroaggregate C (by 50%) and bulk C (host determinism); these shifts were associated with AMF hyphal productivity (50% lower than in wild relatives), soil N and P, and microbial biomass. With a high soil N fertility, the levels of aggregate and bulk soil C were similar between wild relatives and domesticates (plasticity). Despite the limited number of cultivars sampled (n = 10) and the different management practices among sites, our findings suggest domestication effects on ecosystem services, especially those modulated by AMF and soil N fertility. The calculated soil C stocks averaged 99.5 Mg C/ha (range 70–122 Mg C/ha), supporting the possibility of C accrual in breadfruit agroforestry.