Farm-based anaerobic digestion is a promising source of renewable natural gas (RNG), but the carbon intensity of RNG is influenced by methane (CH4) emissions from digestate storage. This study evaluated whether a nutrient recovery system could minimize digestate CH4 emissions from uncovered storage. Nutrients were concentrated in the solid fraction, which contained 82% of the Phosphorus (P) and 39% of the Nitrogen (N) with only 7% of the water. Laboratory results showed that the CH4 emission potential from digestate was 113 ± 6 mL g−1 volatile solids (VS), which was reduced to zero in the liquid fraction after nutrient separation. Measurements from the 0.4-ha uncovered outdoor liquid storage showed CH4 emissions were low, with annual emissions being 1.5% of the CH4 collected by the biodigester. Storage emissions could be further reduced by ensuring that all manure passed through the nutrient recovery system. Overall, the combination of biogas and nutrient recovery reduces the carbon intensity of RNG and improves nutrient distribution.