The scarcity of fertilizers and their rising costs are significant barriers to crop production, as the current agricultural situation in India has shown. In maize–potato–onion cropping systems, the impact of various organic treatments on crop yields and soil parameters has shown that organic treatments increased maize, potato and onion yields compared to chemical treatment (recommended dose of fertilizers) alone. Treatments with applications of different organic sources, each equivalent to 1/3 of the recommended N, along with intercropping of soybeans in maize, radishes in potatoes and coriander in onions, gave the highest yield of maize crops, and significant positive yield trends were observed in four treatments (T1, T2, T4 and T6). Interestingly, all treatments showed a positive effect on potato and onion yields, clearly summarizing potatoes and onions as being more stable crops than maize. Further, the best soil characteristics, viz., bulk density and soil resistance under organic treatment, were lower than those found in integrated and chemical treatments. In contrast, the soil’s water-holding capacity, stable aggregate and infiltration rate followed a reverse trend. The treatment (T3), in which soybeans were grown as an inter-row crop in maize, radishes in potatoes and coriander in onions, showed the highest energy-use efficiency, energy output efficiency and energy productivity.