The full-scale implementation of polyhydroxyalkanoate (PHA) production using mixed microbial cultures (MMCs) has been limited by the low PHA global productivity and overall process yield. This work aimed to demonstrate, at a pilot scale, that by combining different effective operating conditions, it is possible to boost the PHA production performance when using fruit waste as a substrate. The organic loading rate (OLR) and pH of the acidogenic reactor were successfully used as tuning parameters to obtain a high fermentation yield (0.74 gCOD•gCOD −1 ) and a fermentate rich in butyrate, resulting in enhanced PHA production steps. A biomass highly enriched in PHA-storing microorganisms was selected as a result of uncoupling the carbon to the nitrogen feeding. The biomass concentration attained a notable value (7.83 g•L −1 ) as a response to the high OLR (8.7 gCOD•L −1 •d −1 ) imposed. In the PHA accumulation assays, the culture selected at the optimal OLR in the selection reactor achieved a high storage yield (0.98 gCOD•gCOD −1 ), and the continuous feeding strategy led to a maximum PHA content of 80.5% (g-basis). The high global productivity (8.1 g-PHA•L −1 •d −1 ) and overall process yield (0.45 gCOD•gCOD −1 ) are, to the best of the authors' knowledge, the highest values reported for MMC using a real feedstock at pilot scale. These results demonstrate the importance of combining different effective strategies to maximize the process performance, a promising result toward the full-scale implementation of PHA production from wastes and MMC.