Root biomass is the most commonly studied root parameter to investigate below ground crop response to environmental conditions and carbon cycling in agroecosystems. Root growth is strongly regulated by site-specific growth conditions and resource availability, but only little is known about the extent to which root biomass, vertical distribution, and size class respond to fertilization intensity as compared to site. We determined coarse (> 2 mm) and fine (> 0.5 mm and ≤2 mm) root biomass of maize and wheat in three soil layers to 0.75 m depth in different farming systems (half and full organic, full conventional) and fertilization treatments (zero, manure, full mineral N plus half mineral PK, full mineral NPK) of the Swiss long-term field trials DOK and ZOFE, respectively, and evaluated the effects of fertilization intensity and site on root biomass, vertical distribution, and size class. In DOK, total root biomass was similar in organic and conventional farming systems. In ZOFE, wheat root biomass was 1.7-times higher under full mineral N plus half mineral PK fertilization than under zero or manure fertilization and intermediate under full NPK fertilization. Vertical root distribution and size class were only marginally affected by fertilization intensity on both sites. By contrast, total root biomass of maize and topsoil root biomass of both maize and wheat were higher but subsoil root biomass of wheat and fine root proportions of both maize and wheat were lower in DOK than in ZOFE. We conclude that roots respond more to site than to fertilization intensity and that absolute inputs of root biomass carbon to soil are similar in low- and high-intensity systems. Further, root-shoot ratios were inversely related to fertilization intensity, implying that estimations of below ground carbon inputs to soil from shoot biomass need to be differentiated by fertilization intensity. Deep (below 0.5 m) root biomass was 3-times higher for wheat than for maize, suggesting that crop choice is more important than fertilization intensity for carbon sequestration in deep soil.