This paper aims at evaluating the environmental and economic sustainability of bio-refineries that produce multiple products through their supply chains (SCs). A physical enterprise input-output (EIO) model is used to quantify the material/energy/waste flows and integrated to the monetary EIO model to compute the economic performance of bio-refinery SC (BRSC). The empirical case study is based on a (under-construction) bio-refinery which uses thistle oil and residues to produce bio-monomers, bio-lubricants, glycerine, and thermal energy in Porto Torres industrial district, Sardinia (Italy). Given the impact of uncertainty on the performance of the BRSC, we apply sensitivity analysis on the spatial, logistical, and biomass quality variables, i.e., land productivity, transportation distance, and thistle oil content rate. In terms of practical contribution, the physical and monetary EIO models serve as planning and accounting tools for the involved companies of the BRSC. Findings show that the proposed models are effective in evaluating the sustainability of BRSCs and the investigated variables may significantly influence the economic viability of the bio-refinery. From managerial perspective, pricing contracts between the thistle producers and the bio-refinery is critically driven by the transportation distance. The bio-refinery can produce economically competitive outputs with an important contribution to the region's employment market.