Allura red (AR) is a water-soluble synthetic colorant often used as an additive in the food industry, but excess AR can be harmful to human health. In this work, we report the development of a new removal method for AR by using amino-functionalized microspheres with Fe3O4 cores and twolayer shells composed of SiO2 particles and perpendicularly aligned mesoporous SiO2 (designated Fe3O4@nSiO2@mSiO2–NH2). The material exhibits good dispersibility in aqueous solutions and a high saturation magnetization of 45.68emug−1−1, and can be magnetically separated efficiently with an external magnet. Importantly, the material has great adsorption capacity of 29.6mgg−1−1 for AR and the capacity for reuse with a simple treatment. The adsorption process is very fast and the kinetics data are consistent with a pseudo-second order model. Based on these, a rapid and efficient method for extraction and analysis of AR in water and soft drinks has been established.