Simultaneous extraction of multiple clinically relevant, specific allergens from complex, processed foods for immunoassay quantification remains challenging. Moreover, shared extraction buffers remain elusive, which limits the effectiveness of multiplex (multi-target) technology. This study aimed to optimise extraction of specific allergens from challenging food samples and identify shared methods of extraction for multiplex analysis. Incurred processed food matrices (chocolate dessert, raw and baked biscuit) were prepared and extracted with 10 different buffers varying in base, pH, and additive content. Extracts were analysed by allergen-specific multiplex array and ELISA. Optimised recovery of 14 food allergens was obtained from complex incurred matrices using two extraction buffers: 50 mM carbonate bicarbonate with 10% fish gelatine, and PBS with 2%-Tween, 1 M NaCl with 10% fish gelatine and 1% PVP. In most cases, optimised buffers provided 50–150% recovery from incurred foods. Matrices that contained chocolate or were subject to thermal processing had lower recoveries. Optimised allergen extraction methods can be used to analyse foods associated with treatment and prevention of allergy and reference materials for clinically relevant allergen content and identify allergen contamination. Identification of shared, optimised extraction buffers will result in increased sample throughput in multiplex immunoassay techniques.