In rural Ghana, limited access to affordable, clean cooking fuels drives the need for decentralised waste-to-energy solutions. Anaerobic co-digestion (AcoD) offers a viable route for transforming organic residues into renewable energy, with the added benefit of improved process stability resulting from substrate synergy. This study aims to evaluate the technical feasibility and stabilisation challenges of AcoD, using locally available fruit waste and beet molasses at a secondary school in Bedabour (Ghana). Biological methane potential (BMP) assays of different co-digestion mixtures were conducted at two inoculum-to-substrate (I/S) ratios (2 and 4), identifying the highest yield (441.54 ± 45.98 NmL CH4/g VS) for a mixture of 75% fruit waste and 25% molasses at an I/S ratio of 4. Later, this mixture was tested in a 6 L semi-continuous AcoD reactor. Due to the high biodegradability of the substrates, volatile fatty acid (VFA) accumulation led to acidification and process instability. Three low-cost mitigation strategies were evaluated: (i) carbonate addition using eggshell-derived sources, (ii) biochar supplementation to enhance buffering capacity, and (iii) the integration of a bioelectrochemical system (BES) into the AcoD recirculation loop. The BES was intended to support VFA removal and enhance methane recovery. Although they temporarily improved the biogas production, none of the strategies ensured long-term pH stability of the AcoD process. The results underscore the synergistic potential of AcoD to enhance methane yields but also reveal critical stability limitations under high-organic-loading conditions in low-buffering rural contexts. Future implementation studies should integrate substrates with higher alkalinity or adjusted organic loading rates to ensure sustained performance. These findings provide field-adapted insights for scaling-up AcoD as a viable renewable energy solution in resource-constrained settings.