Organic wastes (OW) are rich in nutrients, and their recycling into agriculture can substitute chemical fertilizers. The level of substitution (partial with mineral fertilizer or exclusive with only OW), along with the method, amount, and timing of OW application, as well as the crop type, can impact crop productivity. The temporal dynamics of crop productivity after repeated applications of OW remain uncertain. Thus, two French long‐term field experiments (QualiAgro and PROspective, started in 1998 and 2000, respectively) were used to evaluate the effect of repeated OW applications on crop yield dynamics and investigate the potential driving factors affecting crop yields. Six different OW were applied: urban sewage sludge (SLU), green waste and SLU compost (GWS), biowaste compost (BIO), municipal solid waste compost (MSW), farmyard manure (FYM), and composted FYM (FYMC). The OW were applied every 2 years in QualiAgro (~4 t C ha −1 ) and PROspective (~1.7 t C ha −1 ). QualiAgro was studied under high and low mineral N conditions, while PROspective was examined with and without mineral N fertilization. The results indicated that at the QualiAgro site, a combination of OW and high mineral N treatments resulted in higher maize and wheat yields compared to the mineral N control, while the combination of OW and low mineral N reached the same maize and wheat yield as the mineral N control after 3 and 6 applications of OW, respectively. At the PROspective site, partially substituting mineral fertilizer with OW maintained maize yields but decreased wheat yields, while full substitution led to a decrease in both maize and wheat yields compared to the mineral N control. Results from the gradient boosting model (GBM) showed that soil total N rather than mineral N input was the primary driver of the relative maize yield, while mineral N fertilizer input was more critical for wheat during the second year. We conclude that the joined use of OW and mineral fertilizers is superior to using OW or mineral fertilizer alone for maintaining high yields and soil fertility. We further suggest that OW full substitution of mineral fertilizer may need to apply OW more frequently to meet the crop demands, and/or to use OW with higher N availability like digestates.