Organic field crop systems are characterized by complex rotations with high spatial and temporal vegetative diversity, an enhanced use of legumes, and reduced external nutrient (nitrogen (N) and phosphorus (P)) use. At the same time, a core premise of certified organic agriculture is that this farming system provides benefits to soil health via enhanced microbial diversity. The following short review, drawing primarily upon selected studies from North America, examines the impact of farming systems, and various management strategies within these, on soil organic matter, N and P dynamics, and soil microbial and macrofaunal abundance and diversity. Organic cropping systems are shown to provide benefits with respect to reduced farm N and P surpluses, in combination with maintenance of soil organic matter and improved soil health. However, soil health benefits appear consistently achieved only for larger soil organisms partly due to the resilience of the soil microbial community. Recent research examining soil P dynamics and P uptake in relation to legume biological N2 fixation and bacterial and mycorrhizal community diversity provide evidence of the resilience of the soil microbial community with respect to functionality, if not diversity of microbial community composition. These latter results may challenge organic agriculture core premises of consistent benefits to soil health via enhanced microbial diversity, but in its place may lead to an improved understanding of how specific cropping practices and production system intensity overall, rather than farming system per se, influences both nutrient cycling and soil ecosystem functioning.