Approximately one-third of food produced globally is not consumed but instead lost from the food supply chain. A growing global population, food shortages particularly in Third World countries together with environmental pressures such as water shortage and climate change are placing increasing strains on global food demands. The diversion of food loss back into the food supply chain could provide a significant contribution to meeting these ever increasing food demands. In order to achieve this, however, it is essential to understand the safety and stability of food loss biomass to evaluate its suitability as a new food source. In this study we selected apple pomace, a food loss biomass produced during the production of fruit juices. Apple pomace represents about 30% of the total biomass of an apple and contains the majority of the fibre and protein components. Storage trials were conducted at 4 °C and 8 °C over 7 days to determine the change in microbial load of apple pomace (bacteria, yeast and mould counts), as well as the metabolite profiles (GC-MS). Regardless of storage temperature used, the bacterial community reached similar levels after 7 days, a small reduction in fungal load was achieved at 4 °C relative to 8 °C at 7 days. Analysis of the metabolites showed that despite similar microbial loads, distinct patterns were associated with 4 °C versus 8 °C storage. At 8 °C many of the sensory compounds associated with apple taste and smell were reduced significantly, and this was coupled with a large increase in ethanol suggesting microbial fermentation. In contrast, 4 °C retained these sensory components and limited ethanol production. Taken together these results suggested small changes in storage temperatures drive differences in the microbial population and associated metabolism of stored apple pomace, which may have important consequences for its subsequent utilisation as a food ingredient.