<p>Phosphorus recovery and sustainable nutrient management are increasingly important for agricultural and industrial systems as global phosphate reserves decline. The disruption of the global phosphorus cycle, driven by fertilizer overuse and wastewater discharge, has intensified eutrophication and ecosystem degradation. In biological systems, inorganic phosphate fuels the very essence of life, forming the energetic basis of cellular function. However, fluctuating environmental phosphate conditions compel cells to store this element in the form of polyphosphate inside specialized organelles like acidocalcisomes. Polyphosphate homeostasis varies across microorganisms. Herein, by focusing on yeast and microalgae, this review follows the path of phosphate from its extracellular uptake by high and low affinity transporters (<i>e.g.,</i> Pho89 and Pho90 yeast phosphate transporters; and PTA and PTC families of microalgal phosphate transporters) until its polymerization by Vacuolar Transporter Chaperone complex complex, which represents a functionally comparable polyphosphate synthesis mechanism in these two microbial taxa. Despite extensive research, a comparative overview linking molecular mechanisms to environmental bioprocess performance remains limited. Here, we bridge this gap by synthesizing mechanistic, physiological, and ecological insights to assess the potential of both groups as sustainable phosphorus recovery systems. This review synthesizes multi-omics analyses, structural studies, metabolic modeling approaches, and genome engineering strategies to advance understanding of microbial polyphosphate metabolism and its relevance for phosphorus recovery. Collectively, this review identifies key opportunities for leveraging microbial polyphosphate metabolism to advance environmentally resilient and resource-efficient phosphorus recovery technologies.</p> Graphical abstract <p></p>