Biosolarization is a method for controlling soil pests and pathogens where biomass amendments are incorporated into soil and fermented under thermophilic conditions. Endogenous and fermentative organic acid biopesticides derived from the amendments can disinfest soil without the use of potentially harmful chemical fumigants. However, these biopesticides can be phytotoxic if they linger through crop establishment. This study assessed the phytotoxicity of soils amended with prominent agricultural residues – almond hulls and shells – with and without simulated biosolarization. Germination indices (GI) calculated from radish seedlings were used to measure phytotoxicity of soil amended with 0.3125 to 2.5% biomass by dry weight. Biosolarized soils were initially highly phytotoxic, and GI was negatively correlated to the concentration of succinic, acetic, and lactic acid found in treated soils. Aeration of biosolarized soil successfully improved GI and decreased organic acid concentrations. Decreasing almond residue particle size to less than 0.5 mm also aided phytotoxicity removal for certain biosolarization scenarios. This study concludes that biosolarization with low amendment rates (0.3–0.6%) would be ideal for field application, as they generated high initial organic acid accumulation (27–131 mM), but phytotoxicity could be eliminated after only one week of aeration. The results of this study will be useful for formulating land application strategies for almond residue biomass and addressing a key barrier to adoption for biosolarization as a fumigant alternative.