Two soil amendments, biochar and zeolites, were evaluated in their potential for increasing crop productivity and agro-system sustainability. The effect of biochar and zeolites, in combination with four nitrogen (N) rates [0 (N0), 50 (N50), 100 (N100), and 200 (N200) kg ha−1], on crop yield, N use efficiency, and soil properties was evaluated in a cropping system of irrigated forage maize (Zea mays L.) grown in summer and oats (Avena sativa L.) grown in winter as a catch crop. Biochar increased soil organic carbon (C), pH, cation exchange capacity (CEC), and extractable phosphorus (P), but strongly reduced N recovery in the set of the four cropping cycles. In biochar-amended plots, N50 had a negative apparent N recovery (− 21%), indicating that less N was recovered by the plants than in the N0 treatment without biochar. Biochar reduced maize dry matter (DM) yield by 15.6% in comparison to the untreated control, indicating N immobilization by biochar at low N rates (N0 and N50). Zeolites did not influence crop productivity or soil properties, except for the increase in extractable K, probably the result of its initial K content. N application to maize significantly increased the productivity of both crops, including that of the non-fertilized oats. Under the conditions of this experiment, biochar and zeolites did not prove to be useful soil amendments to increase crop DM yield in the short-term. The use of biochar increased soil organic C, which associated to a high N rate can enable the dual objective of maintaining productivity and the sustainability of the agro-system. The results stressed also the important role of oats as a cover crop to reduce the risk of nitrate leaching and denitrification during winter.