Background Microbial oils - often termed single cell oils (SCOs) - offer an alternative to terrestrial oil crops across the energy, food and chemical industries. In addition to oils, a range of secondary metabolites can be produced from the heterotrophic organisms as part of a biorefinery system. Techno-economic analysis (TEA) is an important tool for evaluating economic viability, and although TEA is subject to high uncertainties where production is still at the laboratory scale, the tool can play a significant role in directing further research to evaluate suitability of scale-up. Results SCO production from the oleaginous yeast Metschnikowia pulcherrima using sucrose, wheat straw and distillery waste feedstocks was evaluated at two production scales. At a scale of 100 t year(-1) oil production a minimum estimated selling price (MESP) of euro14 000 t(-1) was determined for sucrose. This reduced to euro4-8000 t(-1) on scaling to 10 000 t year(-1), with sucrose and wheat straw yielding the lowest MESP. Conclusions Feedstock price and lipid yield had the greatest impact on overall economic return, though the valorization of co-products also had a large effect, and further play between feedstock and system productivity strategies could bring the price down to be competitive with terrestrial oils in the future. The novel approach demonstrated here for the first time integrates uncertainty into economic analysis whilst facilitating decision-support at an early technology development stage. (c) 2018 Society of Chemical Industry