The accumulation of allelochemicals in farming land has attracted a great deal of research attention, and biochar has shown positive effects in alleviating allelopathy. This study investigated how oligotrophic biochar application modulated salicylic acid (SA) generation in soybean roots through nutrient and oxidative stress pathways. Biochars were applied to soybean cultivation, with analyses conducted on nutrient adsorption, allelochemical profiles, and plant growth parameters. Results revealed that biochar suppressed benzoic acid (BA) while elevating SA levels, which correlated with the presence of persistent free radicals (PFRs) and nutrient retention. The retention of phosphorus (P) and ammonium (NH₄⁺-N) dominated plant height reduction, surpassing oxidative stress effects linked to PFRs. Multivariate linear regression (MLR) identified P retention as the primary driver of SA generation, linked to adaptive phosphorus solubilization via acid secretion. Conversely, malondialdehyde (MDA) accumulation resulted from lipoxygenase-mediated lipid peroxidation under nutrient stress and PFRs-induced oxidative stress. The strong adsorption of P and nitrate (NO₃⁻-N) by biochar exacerbated soil oligotrophy, triggering SA overproduction as a stress compensation mechanism. The significant correlation between SA and MDA indicated bidirectional stress signaling, wherein allelochemicals exacerbate oxidative damage while activating defense responses. These findings emphasize the dual role of biochar as both a stress inducer and an allelopathy modulator, highlighting the necessity for optimizing pyrolysis and developing soil-specific strategies to balance agricultural benefits with ecological risks.