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The quality of soil plays a crucial role in sustainable agriculture. To better understand the changes in soil quality across different agroecosystems, long‐term experiments are considered as the most effective approach. Moreover in spite of their significance, there is paucity of information pertaining to long‐term impact of fertilizer and manure application on soil quality in Vertisols of Central India. Thus, the present study aimed to assess the soil quality in an ongoing 46‐year long‐term fertilizer experiment conducted in central India, where a soybean‐wheat cropping system (SWCY) was implemented on a Vertisol. The experiment involved the application of inorganic and integrated nutrient treatments, including farmyard manure (FYM). By analyzing various biological and physiochemical properties of the soil, a soil quality index (SQI) was developed. The SQI encompassed treatments with both optimal and suboptimal nutrient dosages, revealing the range of soil quality variations resulting from different nutrient applications over the long term. The study found a significant correlation between the SQI values and the grain yields of soybean (R2 = 0.85**) and wheat (R2 = 0.85**). The main indicators identified for assessing soil quality were large macro‐aggregates, dehydrogenase activity, microbial biomass nitrogen and carbon, and available nitrogen. Overall, the findings highlighted the importance of soil biological and physiochemical properties in determining soil quality, emphasizing the significance of integrating both inorganic and organic sources of nutrients for improving soil quality and crop productivity of soybean and wheat sequence in Vertisols of Central India. [ABSTRACT FROM AUTHOR]