Isolation of individual pharmaceutical-grade bioactive compounds from complex plant extracts is still a sustainability challenge. Process intensification improves manufacturing design to achieve significant benefits in process efficiency and operation, product quality, and waste management. A process optimization and intensification methodology for the simultaneous isolation of biophenols from agricultural waste using imprinted materials and nanofiltration membranes is reported herein. First, temperature-swing molecular imprinting technology was used to selectively extract individual biophenols from olive leaf extracts.Second, solvent-resistant nanofiltration was used to in line concentrate the product and waste streams as well as recover the solvent. The predictive mathematical models for the adsorption dynamics and the membrane separation resulted in a significant reduction in the carbon footprint, E factor and economic sustainability. The process was designed for easy operation with multi-way valves to aid safety and reduce operating costs. The presented process intensification methodology can be generally exploited for waste upcycling through sustainable isolation of multiple high-value products from complex mixtures.