Conventional manure storages are an important source of methane (CH4), a potent greenhouse gas. Anaerobic digestion is an alternative manure management practice potentially able to provide environmental benefits, including the reduction of CH4 emissions from slurry storage. This study was conducted at a commercial farm in Ontario where a biodigester system became operational in May 2012. The purpose was to quantify year-round CH4 emissions from a digestate storage tank, examine the relationship between emissions and its driving factors, and compare these results to a similar emissions dataset from untreated manure measured during one year before the biodigester became operational. A micrometeorological mass balance approach was used to measure CH4 fluxes. Total annual CH4 emissions from digestate were 1.0 kg m−3 y−1, which was 85% lower compared to untreated manure. Monthly average volatile solids (VS) mass in the storage tank was 73 ± 24 Mg for digestate and 107 ± 30 Mg for manure, representing a 32% VS reduction in the tank, suggesting that lower emissions were not only due to VS mass reduction after biodigestion and solid-liquid separation. The annual CH4 emissions scaled by VS were 26 g kg−1 VS y−1 for digestate and 76 g kg−1 VS y−1 for manure, suggesting that VS in the digestate were less suitable for CH4 production (less digestible). This was also verified when investigating the relationship between fluxes and its driving factors: VS concentration did not correlate with CH4 emissions per volume for digestate (r = 0.37; p = 0.29), but did for untreated manure (r = 0.95; p = 0.002). However, the correlation of temperature with emission was stronger for digestate than manure at all depths with no lag, especially at 2 m depth (r = 0.98, p < 0.001). At the same air temperature, digestate was warmer than manure, owing to the digestate leaving the digester at 38 °C. This study showed that co-digestion of dairy manure and off-farm materials (35% of loading volume) with a 60-day hydraulic retention time and subsequent solid liquid separation significantly reduced facility-scale CH4 emissions from the storage tank.