Food production systems can contribute to the degradation of the environment; thereby endangering the very resource, they depend on. However, while overall large, the environmental impacts of individual agricultural products are disparate. Therefore, in order to gain a better understanding of the impact different food production systems have on the environment, we should start at the produce level. In this study, we combine life cycle assessment (LCA) methodology and data envelopment analysis to calculate environmental efficiency scores (i.e., agricultural output divided by environmental impacts) for eight product groups (Milk, Cattle, Pig fattening, Cereals, Beets, Potatoes, Vegetables, Fruits) in Switzerland. First, LCA is used to calculate “cradle to farm-gate” environmental impacts. These impacts are then used as inputs in a data envelopment analysis, with the amount of produced agricultural products as outputs. The resulting environmental efficiency scores reflect the relative efficiency (i.e., related to the best-observed performance) of the observed product groups. We find large differences in environmental impacts and environmental efficiency score distribution between the product groups. While we find some variability of environmental efficiency between farming systems (Organic and Proof of Ecological Performance) within a product group (difference in coefficient of variation between farming systems: Fruits = 48%, Vegetables = 13%, Cereals, Potatoes = 8%), we did not find any significant differences in environmental efficiency between organic and integrated farming systems for any of the considered product groups. Furthermore, we did not find a negative effect of multifunctionality of Swiss farms (i.e., multiple simultaneously produced product groups), but found a small positive effect for Milk in the presence of other product groups. However, the high within product group variance of environmental efficiency suggests the potential for improvements (notably >40% for Fruits and >30% for Cattle and Potatoes).