Buckwheat microgreens have short shelf life which limits their commercial use. The effects of storage temperature, modified atmosphere packaging (MAP), and wash conditions on quality and shelf life of buckwheat microgreens were assessed. Temperature significantly (P < 0.0001) affected package atmospheres and product quality. At the end of storage, microgreens stored at 1, 5 and 10 °C had smaller microbial populations and less tissue electrolyte leakage than those stored at 15, and 20 °C. Package film oxygen transmission rate (OTR) significantly (P < 0.05) affected package atmospheres. However, differences in quality and shelf life of microgreens packaged in different OTR films were slight and not evident until day 21 of storage. On day 21, buckwheat microgreens packaged in 16.6 pmol/(m2 s Pa) oxygen transmission rate package films were observed to have the freshest appearance with lowest tissue electrolyte leakage. Chlorine (100 mg/L) wash significantly (P < 0.05) reduced microbial populations, initially; however, after 7 days of storage, all washed microgreens experienced accelerated microbial populations. Our findings suggest that buckwheat microgreens should be stored at 5 °C with moderately high O2 (14.0–16.5 kPa) and moderately low CO2 (1.0–1.5 kPa) content to maintain optimal quality and maximal shelf life.