BACKGROUND: Bacteriophages are bionanoparticles with several applications in different biotechnology-based products. Among them, vaccines have the potential to treat antibiotic-resistant bacteria and parasitic infections. Traditional methods for their recovery and purification rely on precipitation with polyethylene glycol (PEG) and NaCl. However, the applicability of such an approach is limited, due to large-scale technical constrains. Recently, our research group developed a bacteriophage M13 recovery and purification strategy using Aqueous Two-Phase Systems (ATPS), simplifying the methodology and, potentially, reducing costs. This work aims to develop an economic contrast between ATPS and the traditional PEG precipitation method at different operation scales (10 to 1000 L bioreactor volume) to determine the applicability of the ATPS methodology at large scale. For this, the effect of ATPS volume ratio (V R), sample loading, and materials discount over production cost were analyzed. RESULTS: Results indicate that as the discount on material costs increases, ATPS becomes a more affordable unit operation, from a bioreactor scale of 10 L at 0% discount to 410 L at 90% discount (US$ 52.2 to $1.72 per gram, respectively). Material cost contribution is a parameter that needs attention when working with ATPS, as it is the core for the system construction. Methods for reducing their contribution are highly relevant and should be further investigated. CONCLUSION: Employment of economic analyses help to discover critical parameters for a bioprocess, such as material costs for ATPS. This economic analysis work serves as a platform for new strategies for the recovery of bacteriophage and bacteriophage-like particles using ATPS-based technologies.