Net zero as a policy for reducing atmospheric carbon emissions is relatively straightforward; however, the implementation of that policy is not, particularly in difficult-to-measure sectors such as agriculture. As strategies to reduce emissions are explored, multiple uncertainties in measuring these emissions are confronted. In this paper, we use the example of a coffee supply chain in Peru to illustrate the magnitude of potential variability in emissions accounting results, which represent a necessary first step in moving towards net zero. We show that scope boundaries and emissions factors chosen for carbon calculations significantly alter emissions outcomes and can result in discrepancies of over 77 million kg CO2e when scaled to a medium-size coffee trader. Net zero targets and efforts to reduce emissions may be over- or understated depending on subjective decisions that cause significant differences in emissions results. Although framework guidance exists, it is apparent that a greater set of micro-level agreements is needed for calculating the emissions of lesser-studied sectors, such as agricultural supply chains. This process is imperative to focus efforts on reducing emissions and on moving from net zero as a mere policy to action and implementation.