This study examined using peanut shells, rice husks, and cocoa husks as soil conditioners to boost yields in Allium cepa var. Alvara onions. Three types of biochar and four application rates (1%, 1.5%, 3%, and 5%) were compared to a control with no biochar. The biochars had different nutrient makeups, with cocoa husk biochar (CHB) containing the most essential elements. While overall plant growth (height, leaves, and roots) was not significantly affected (p > 0.05) by any biochar type compared to the control, some plant parts responded differently. CHB (5%) and peanut husk biochar (PHB) (1%) yielded the tallest onion plants (71 and 65 cm), while 1% rice and cocoa biochar resulted in the shortest (below 42 cm). PHB (3% and 5%) produced the longest roots (9 cm), while 1.5% rice husk biochar (RHB) had the shortest. Biochar application had no significant effect on leaf count. However, specific application rates of RHB and PHB increased the harvest index (HI), indicating more efficient yield allocation. HI values > 0.85 were obtained with specific biochar rates (e.g., 1.0–1.5% PHB, 1.5–5% RHB, or 5.0% CHB).