Chestnuts are a widely consumed fruit around the world, with Portugal being the fourth biggest producer in Europe. Storage of these nuts is an important step during processing, and the most widely used fumigant was banned in the European Union under the Montreal Protocol because of its toxicity. Recently, radiation has been introduced as a cheap and clean conservation method. Previous studies of our research group proved that γ radiation had no negative effect on the nutritional value of chestnuts; in fact, storage time had a much bigger influence on the chestnut quality. In the present study, we report the effect of a less ionizing radiation, electron beam, with doses of 0, 0.5, 1, 3, and 6 kGy in the nutritional value of chestnuts (ash, energy, fatty acids, sugars, and tocopherols), previously stored at 4 °C for 0, 30, and 60 days. The storage time seemed to reduce fat and energetic values but reported a tendency for higher values of dry matter. With regard to fatty acids, there was a higher detected quantity of C20:2 in non-irradiated samples and four fatty acids were only detected in trace quantities (C6:0, C8:0, C10:0, and C12:0). γ-Tocopherol decreased during storage time but did not alter its quantity for all of the radiation doses (as like α-, β-, and δ-tocopherol); in fact, these compounds were present in higher concentrations in the irradiated samples. Sucrose and total sugars were lower in non-irradiated samples, and raffinose was only detected in irradiated samples. Electron-beam irradiation seems to be a suitable methodology, because the effects on chemical and nutritional composition are very low, while storage time seems to be quite important in chestnut deterioration.