Food analysis is requiring rapid, accurate, sensitive, and cost-effective methods to monitor and guarantee the safety and quality to fulfill the strict food legislation and consumer demands. In this study, a nano-materials enhanced multipurpose paper-based microfluidic aptasensor was developed as a sensing tool for accurate detection of food allergens and food toxins. graphene oxide (GO) and specific aptamer-functionalized quantum dots (QDs) were employed as probes, the fluorescence quenching, and recovering of the QDs caused by the interaction among GO, aptamer-functionalized QDs, and the target protein were investigated to quantitatively analyze the target concentration. The homogenous assay was performed on the paper-based microfluidic chip, which significantly decreased the sample and reagent consumption and reduced the assay time. Egg white lysozyme, ß-conglutin lupine and food toxins, okadaic acid and brevetoxin standard solutions, and spiked food samples were successfully assayed by the presented aptasensor. Dual-target assay was completed within 5 min, and superior sensitivities were achieved when testing the samples with commercial enzyme linked immunosorbent assay kits side by side. Practical applications: The present aptasensor provides a simple, accurate method for rapid quantitative analysis of allergens or toxins in food. This method is able to achieved rapid on-site detection of potential allergen/toxin contaminations, which is a critical necessity for individuals with food allergies and other types of food sensitivities. In addition, the present method can be easily implemented into routine analysis to help food producers and regulations secure the safety and compliance of food products.