Sample preparation is a relevant step in food analysis to achieve adequate extraction and preconcentration of target analytes before their introduction in the analytical system. Current trends in sample preparation involve moving towards miniaturized extraction devices combined with advanced affinity-based sorbents. Within affinity-based materials, aptamer-based ones have attracted much attention due to their excellent molecular recognition properties, high stability, and the possibility of immobilization onto the surface of different supporting materials, such as nanoparticles, monolithic stationary phases, etc. This review gives an overview of the literature published regarding aptamer-based sorbents and their potential application in the isolation and determination of several compounds such as persistent organic pollutants (POPs), antibiotics, toxins and bacteria in different food matrices. For this purpose, the most relevant improvements achieved in the last five years (from 2016 to 2020) in sample preparation by the integration of these new materials as sorbents in different miniaturized extraction techniques will be reviewed.