The use of residual streams as feedstock for the production of polyhydroxyalkanoates (PHAs) is growing steadily, as it allows the valorization of waste and nutrients otherwise disposed of and the potential production of a biodegradable bioplastic. To date, the environmental and economic costs associated with this process limit its scale-up, which is why it is important to identify possible solutions and optimize the costliest steps. With this in mind, a laboratory-scale sequenced batch reactor (SBR, 5 L) was constructed to allow the selection of a mixed microbial culture able to convert volatile fatty acids (VFAs) into PHA. The reactor is fed with synthetic water containing VFAs, ammonium, phosphate, and micronutrients, typical compounds of fermented streams of certain wastes, such as cheese whey, food waste, or wastewater sludge. The biomass selected and produced by this first reactor is sent to an accumulation reactor, which is fed with a solution rich in VFAs, allowing the accumulation of PHAs. The role of aeration and its impacts on the main process parameters were analyzed. Three scenarios corresponding to different aeration rates were analyzed: 0.08, 0.16, and 0.32 vvm. The SBR was operated at an organic load rate of 600 mgCOD L−1d−1, under a dynamic feeding regime (feast–famine) and a short hydraulic retention time (HRT; 1 day). The results obtained showed that a value of 0.32 enabled better selection and better settling of the sludge. Furthermore, a potential correlation between aeration rate and VFA and NH4+ consumption rates was identified. The resulting biomass was able to accumulate up to 0.15 ± 0.02 g PHAgVSS−1.