Recycling of nutrients through soil application of bioenergy by‐products (BEBPs) promotes closing of nutrient cycle as well as solves issues related to their improper management. Present investigation reports experimental data on soil fertility, crop growth (rapeseed), and crop nutrition from application of 15 fertilization treatments comprising of 13 BEBPs treatments, NPK and control. The selected by‐products are three types of digestates from anaerobic digestion namely, (i) cowdung, (ii) co‐digested Ipomoea carnea leaves:cowdung (60:40 dry weight), (iii) co‐digested rice straw:green gram stover:cowdung (30:30:40 dry weight) and one char (Rice husk) from gasification system. Fertilizer potential of digestates are assessed in four application phases namely, whole, separated solid, separated liquid, and ash from solid digestates. Significant variations in soil parameters (pH, EC, soil organic carbon, soil available N, P, and K, soil micronutrients) and crop responses were seen with respect to both feedstock type and application phases. BEBP application particularly in solid and whole phase proved significantly better in improving soil organic carbon. Addition of BEBP resulted in increased aboveground productivity, crop yield, plant NPK concentration compared with BEBP unfertilized condition. Overall, the improvement in grain yield over BEBP untreated control can be related to improvement in soil fertility (available fraction of N, P, and K), organic carbon, pH as well as crop physical growth. This study demonstrated that, due to differential partitioning of nutrients, a differentiated planning of BEBP applications, governed by the nature of feedstock and phase of applications would be required. © 2018 American Institute of Chemical Engineers Environ Prog, 38:e13099, 2019