The agri-food sector generates substantial quantities of waste material on farm and during the processing of these commodities, creating serious social and environmental problems. However, these wastes can be resources of raw material for the production of valuable chemicals with applications in various industrial sectors (e.g., food ingredients, nutraceuticals, bioderived fine chemicals, biofuels etc.). The recovery, purification and biotransformation of agri-food waste phytochemicals from this microbial spoilage-prone, complex agri-food waste material, requires appropriate fast pre-treatment and integration of various processes. This review provides a brief summary and discussion of the unique advantages and the importance of membrane technology in sustainable recycling of phytochemicals from some of the main agri-food sectors. Membrane-based pressure -driven processes present several advantages for the recovery of labile compounds from dilute streams. For example, they are clean technologies that can operate at low temperature (20–60 °C), have low energy requirements, there is no need for additional chemicals, can be quite automated and electrifiable, and have low space requirements. Based on their permselective properties based on size-, shape-, and charge-exclusion mechanisms, membrane-based separation processes have unpaired efficiency in fractionating biological components while presenting their properties. Pressure-driven membrane processes, such as microfiltration (MF), ultrafiltration (UF) and nanofiltration (NF), as well as other advanced membrane-based processes such as membrane bioreactors (MBR), membrane emulsification (ME) and membrane distillation (MD), are presented. The integration of various membrane technologies from the initial recovery of these phytochemicals (MF, UF, NF) to the final formulation (by ME) of commercial products is described. A good example of an extensively studied agri-food stream is the olive processing industry, where many different alternatives have been suggested for the recovery of biophenols and final product fabrication. Membrane process integration will deliver in the near future mature technologies for the efficient treatment of these streams in larger scales, with direct impact on the environmental protection and society (production of compounds with positive health effects, new job creation, etc.). It is expected that integration of these technologies will have substantial impact on future bio-based societies over forthcoming decades and change the way that these chemicals are currently produced, moving from petrochemical-based linear product fabrication to a sustainable circular product design based in agri-food waste biomass.