Traditional plastics have undoubted utility and convenience for everyday life; but when they are derived from petroleum and are non-biodegradable, they contribute to two major crises today’s world is facing: fossil resources depletion and environmental degradation. Polyhydroxyalkanoates are a promising alternative to replace them, being biodegradable and suitable for a wide variety of applications. This biopolymer accumulates as energy and carbon storage material in various microorganisms, including microalgae. This study investigated the influence of glucose, N, P, Fe, and salinity over the production of polyhydroxyalkanoate (PHA) by Scenedesmus sp., a freshwater microalga strain not previously explored for this purpose. To assess the effect of the variables, a fractional Taguchi experimental design involving 16 experimental runs was planned and executed. Biopolymer was obtained in all the experiments in a wide range of concentrations (0.83–29.92%, w/w DW), and identified as polyhydroxybutyrate (PHB) by FTIR analysis. The statistical analysis of the response was carried out using Minitab 16, where phosphorus, glucose, and iron were identified as significant factors, together with the P-Fe and glucose-N interactions. The presence of other relevant macromolecules was also quantified. Doing this, this work contributes to the understanding of the critical factors that control PHA production and present Scenedesmus sp. as a promising species to produce bio-resources in commercial systems.