Purpose <p>Imbalanced nutrient application threatens soil health and crop productivity, necessitating balanced integrated nutrient management (INM) for potato (<i>Solanum tuberosum</i>)-maize (<i>Zea mays</i>) (fodder)-maize system to ensure sustainability.</p> Methods <p>Field experiment with fourteen INM treatments and three replications, comprising different combinations of percent-varied doses of recommended FYM (Farmyard manure) and chemical fertilizers (CF), with or without phosphate-solubilizing bacteria (PSB) in potato, consortium in maize (fodder) and cowpea retention in maize was conducted in randomized complete block design at Punjab Agricultural University, Ludhiana, Punjab, India during 2021–2022 and 2022–2023.</p> Results <p>The results indicated that treatment T₈ [75% recommended FYM + 100% recommended CF in potato, 75% recommended FYM + 75% recommended CF + consortium in maize (fodder) and 75% recommended FYM + 75% recommended CF + cowpea retention in maize], being at par with the treatments of recommended doses of FYM and CF (T₁₁ and T₁₂), significantly improved the soil properties viz. Physical [bulk density (1.34&#xa0;g cm^− 3) and water holding capacity (42.68%)], chemical [organic carbon (0.46%), available macronutrients and micronutrients] and biological (microbial count, enzymatic activity, microbial biomass dynamics) over other treatments. The correlation matrix of soil properties showed significant associations, while correlation and regression analysis indicated that system productivity was strongly responsive to soil properties.</p> Conclusion <p>Balanced fertilization through INM treatment T₈ is recommended for the potato-maize (fodder)-maize system, as it significantly improved soil health and increased system productivity (269.43 q ha^− 1), resulting in higher net returns (USD 3466 ha^− 1) and BC ratio (1.45) with reduced input compared to other treatments.</p>