Germination can be used to improve the texture and flavor of cereals. However, germination generally causes breakdown of β‐glucans, which is undesirable with respect to the functional properties of β‐glucan. Our aim was to assess possibilities of germinating oat without substantial loss of high molecular weight β‐glucan. Two cultivars, hulled Veli and hull‐less (naked) Lisbeth were germinated at 5, 15, and 25°C and dried by lyophilization or oven drying. Elevated germination temperatures led to an increase in Fusarium, aerobic heterotrophic bacteria, Pseudomonas spp., lactic acid bacteria, enterobacteria, and aerobic spore‐forming bacteria. Therefore, the germination temperature should be kept low to avoid excessive growth of microbes. Of the samples germinated at 15°C, only one contained low amounts of the Fusarium toxin deoxynivalenol (52 μg/kg). Germination led to the breakdown of β‐glucans, but the decrease in the molecular weight of β‐glucan was initially very slow. A short germination schedule (72 hr, 15°C) terminated with oven drying was developed to produce germinated oat with retained β‐glucan content. Compared with the native oat, 55–60% of the β‐glucan could be retained.