A sustainable polycogeneration prototype (TRL6) was designed and built for simultaneous and decentralized generation of electricity, distilled water, biofuel, and other possible output. The prototype installed at the Federal University of Rio de Janeiro (UFRJ) consists of a high concentration photovoltaic panel (HCPV), which converts solar energy into electricity, conventional planar solar collectors, a thermal control tank, a commercial desalination system via membrane distillation, and a microreactors-based biodiesel continuous synthesis process. In the HCPV system, part of the solar energy incident through the Fresnel lens that is not converted into electricity, is recovered as waste heat through micro-heat exchangers installed at the substrate of the photovoltaic cells. Then, together with the available heat from the solar collectors, either operating in series or in parallel with the thermohydraulic circuit of the HCPV system, the recovered thermal energy drives the air-gap membrane water distillation (V-AGMD) and the micro-reactors for ethanol-based biodiesel synthesis. In the MD process, the required temperatures are generally low, between 50° and 90°C, allowing for the recovery of low-grade waste heat, which is generally difficult to reuse or of low economic value for other secondary processes. Similarly, the transesterification reaction within the micro-reactors is markedly enhanced by integrating micro-heat exchangers to these modular micro-devices, with typical temperatures around 60°C. The present work describes the prototype and the associated thermal processes, providing theoretical and experimental analysis of the individual devices and of the integrated system.