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Abstract Conservation agriculture (CA)-based practices have been promoted and recouped, as they hold the potential to enhance farm profits besides a consistent improvement in soil properties. A 7 years' field experiment consisting of three crop establishment practices viz., zero-till flatbed (ZTFB), permanent beds (PNB), conventional system (CT) along with the three-nutrient management; nutrient expert-based application (NE), recommended fertilization (RDF), and farmers’ fertilizer practice (FFP), was carried out from 2013 to 2020. The CA-based practices (ZTFB/PNB) produced 13.9–17.6% greater maize grain-equivalent yield (MGEY) compared to the CT, while NE and RDF had 10.7–20% greater MGEY than the FFP. PNB and ZTFB gave 28.8% and 24% additional net returns than CT, while NE and RDF had 22.8% and 17.4% greater returns, respectively over FFP. PNB and ZTFB had 2.3–4.1% (0.0–0.20 m soil layers) lower bulk density than the CT. Furthermore, microbial biomass carbon (MBC) increased by 8–19% (0.0–0.50 m soil layers) in ZTFB/PNB over the CT, and by 7.6–11.0% in NE/RDF over FFP. Hence, CA-based crop establishment coupled with the NE or RDF could enhance the yields, farm profits, soil properties of the maize–chickpea rotation, thereby, could sustain production in the long run.