In this study, life cycle assessment (LCA) methods are used to develop life cycle inventory (LCI) and life cycle impact assessment (LCIA) data to estimate the global warming potential (GWP) and energy intensity (EI) of cheese and dry whey manufacturing in Wisconsin using a farm gate to plant gate approach. All of the environmental burdens and benefits are assigned to the product (cheese) and none are assigned to the land-spread waste stream (whey) for a single-output system typical of small cheese plants in Wisconsin. For a multifunction system, in which both cheese and food-grade whey are produced, the following methods are applied to handle co-product multifunctionality: subdivision, allocation ratios, and a method that combines both subdivision and allocation ratios. Total solids, nutritional content, and economic value are considered as the allocation ratios. Each of these fixed allocation ratios is applied to the entire process and to individual processes unique to each product. The differences in the GWP and EI for cheese and dry whey are highly influenced by the choice of method. The EI of cheese ranges from 7.1 to 19 MJ kg-1 cheese, and the GWP of cheese ranges from 0.46 to 1.3 kg CO2-eq kg-1 cheese. The main source of these differences is the shift of environmental burdens from cheese to the dry whey co-product resulting from different allocation strategies. The method that combines subdivision and allocation is presented as the preferred and most accurate method to deal with the multifunctionality of cheese and whey manufacturing. Sensitivity analysis shows that GWP and EI are most affected by variations in milk pasteurization, whey evaporation, whey drying, and whey pasteurization. This study demonstrates the importance of the allocation method on LCA analysis and suggests methods to more accurately assess the environmental burdens when more than one product is produced at a dairy plant.