For half a century aqueous two‐phase systems (ATPSs) have been applied for the extraction and purification of biomolecules. In spite of their simplicity, selectivity, and relatively low cost they have not been significantly employed for industrial scale bioprocessing. Recently their ability to be readily scaled and interface easily in single‐use, flexible biomanufacturing has led to industrial re‐evaluation of ATPSs. The purpose of this review is to perform a SWOT analysis that includes a discussion of: (i) strengths of ATPS partitioning as an effective and simple platform for biomolecule purification; (ii) weaknesses of ATPS partitioning in regard to intrinsic problems and possible solutions; (iii) opportunities related to biotechnological challenges that ATPS partitioning may solve; and (iv) threats related to alternative techniques that may compete with ATPS in performance, economic benefits, scale up and reliability. This approach provides insight into the current status of ATPS as a bioprocessing technique and it can be concluded that most of the perceived weakness towards industrial implementation have now been largely overcome, thus paving the way for opportunities in fermentation feed clarification, integration in multi‐stage operations and in single‐step purification processes. Aqueous two‐phase systems (ATPS) are approached through a novel SWOT (Strengths, Weaknesses, Opportunities and Threats) perspective, where their potential for integration in industrial bioprocesses is evaluated based on classic knowledge and recent advances in this field. Overall, it can be concluded that ATPS weaknesses towards industrial implementation have been largely overcome, paving the way for opportunities in feed clarification, multi‐stage operation and single step purifications.