Kura clover living mulch (KCLM) can be integrated into Midwestern row-crop production systems as a soil and water conservation tool. Rotary zone tillage is currently recommended to establish a clover-free zone for maize seeding in the living mulch, however, this practice is costly and presents a major barrier to producers. Banding anhydrous NH3 in a KCLM, due to its transient caustic impact, may damage clover roots and provide supplemental clover suppression. This experiment aimed to determine the effects of tillage intensity and fertilizer source on maize yield and clover root biomass. Maize was seeded into a KCLM prepared with rotary zone tillage (RZT) or shank strip tillage (ST) and fertilized with ammonium nitrate (NH4NO3) or NH3 banded under the tilled zone. Aboveground clover biomass, total root biomass, and soil N were sampled at eight times between tillage and the R4 maize physiological growth stage, and maize and clover roots were differentiated using their 13C isotope signatures. Results indicated that ST achieved adequate clover suppression and grain yields were not affected by tillage or fertilizer treatments. The RZT treatment reduced clover root biomass relative to ST, but fertilizer N source did not affect above or belowground clover biomass pools. Based on the results of this study, we conclude that ST can be used with any form of banded N fertilizer to successfully manage maize in KCLM while maintaining a greater level of clover root biomass than RZT.