This study analyzed economic feasibility of implementing anaerobic digestion for waste treatment of manure and whey from an artisan cheese making operation combined with a small-scale dairy farm. Enterprise budgets were used to calculate net present value (NPV) and internal rate of return (IRR) from equipment price quotes, estimations from literature and using estimated annual receipts and costs for a 210-cow dairy farm in Utah, an artisan cheese plant producing bottled milk and cheese, and an inverted bed reactor anaerobic digester to handle manure and whey. Each enterprise was analyzed separately and integrated together to provide hypothetical models of annual costs and returns that can be viewed as a tool to help farmers make decisions about investments. Total costs for the dairy farm was $758,538 and based on 2015 milk prices this provided a net income (NI) of -$371 per head of cow. Initial investment cost for the artisan milk processing, cheese making and retail facility was $1,658,984 ($7,900 per head). Total operating costs were $898,835 with NI of $198,020 ($943 per head). How the cheese is marketed impacts NI as cheese can be sold directly by the artisan cheese maker (either through a retail store or online) at $29/kg compared with $17/kg or $9/kg if sold wholesale or through a distributor, respectively. Total cost for the anaerobic digester was $320,621 (after a 10% investment tax credit) that equates to $1,527 per head. Total operating cost was $66,238 with NI of $2,105 ($10/head) based on electricity generated and sale of digester biomass, carbon offsets and services for managing digestion of whey, manure and other organic wastes. For adding an artisanal cheese making facility producing 47,000 kg of cheese per year, NPV was estimated at $580,739 with 39% IRR. In comparison, NPV for the digester system was -$65,378 with IRR of −5.2%. For investment in a digester to be acceptable, a 12% discount rate is needed, meaning that 35% of the investment cost must be subsidized. Currently, small-scale dairy farmers facing urban encroachment cannot economically adopt anaerobic digestion to manage waste without an appropriate investment subsidy reflecting its social value.