A growing number of plant-based milk substitutes have become commercially available, providing an array of options for consumers with dietary restrictions. Though several of these products rival cow’s milk in terms of their nutritional profiles, beverages prepared with soy and tree nuts can be a significant concern to consumers because of potential contamination with food allergens. Adding to this concern is the fact that allergen residues from plant-based beverages are modified during manufacturing, thereby decreasing the sensitivity of antibody-based detection methods. Consequently, many commercially available allergen detection kits are less effective for allergens derived from nondairy milk substitutes. To address this limitation, we developed a panel of polyclonal antibodies directed against the modified proteins present in almond, cashew, coconut, hazelnut, and soy milks and incorporated them into rapid lateral flow immunoassay tests configured in both sandwich and competitive format. The tests had robust detection capabilities when used with a panel of various brand-name products, with a sensitivity of 1 ppm and selectivity values of 3 to 5 ppm in nondairy beverages. Minimal cross-reactivity to extracts prepared from common commodities was observed. The development of a highly sensitive and rapid test specifically designed to detect trace quantities of highly modified allergen residues in plant-based, dairy-free beverages will aid food manufacturers and regulatory agencies in monitoring products for these modified allergens when testing environmental and food samples.