Storage conditions influence the nutritive value and quality of many legumes. The aim of this study was to evaluate the quality of beans stored under hermetic conditions as a strategy for preserving the quality of beans post-harvest. Three bean varieties [
Rosecoco
, small red (
Wairimu
)], and red mottled (
Nyayo
)] were adjusted to three moisture levels (12%, 15% and 18%) and stored in hermetic bags and ordinary polypropylene bags and sampled after 0, 45, 90, 135,180, 225 and 270 days for chemical and anti-nutritional analysis. Total soluble sugars,
in-vitro
starch and protein digestibility, free amino nitrogen, tannin content and phytic acid content of the beans were determined using standard methods. Results showed that the beans in hermetic bags had 22%, 23% and 18% higher total soluble sugars,
in-vitro
starch and protein digestibility, respectively, than those in polypropylene bag during storage. On day 225 of storage, beans in hermetic bags had the optimal
in-vitro
starch and protein digestibility, and tannin content. Principal component analysis indicated that nutrient and anti-nutrient retention of the beans was achieved with lower storage moisture and duration in hermetic bags. The results of this study can be used to explain the superiority of the hermetic storage technology over ordinary methods of beans storage, and by extension other legumes, in nutrient retention during storage.