The aim of this study was to determine the influence of the nut roasting process (conventional and microwave methods) and long-term storage (12 months) on phytosterol content and stability. This study was conducted using hazelnuts (Corylus avellana), common walnuts (Juglans regia L.), and shelled peanuts (Arachis hypogaea L.). Two roasting methods were examined: conventional (temp. 170 °C, roasting time 10–20 min.) and microwave (temp. 60 °C, pressure 40 hPa, roasting time 140–180 s). In the studied nuts (raw, roasted and stored), five main types of phytosterols were identified: campesterol, stigmasterol, ß-sitosterol, delta 5-avenasterol and cycloartenol. It was shown that the microwave roasting method caused a two-fold decrease in sterol loss compared with conventional roasting. Moreover, the long-term storage of roasted walnuts using the microwave method showed double the amount of sterols preserved compared with those roasted using the conventional method. The amount of ß-sitosterol, which was the most stable during roasting, depended more on storage duration than on roasting process. The cycloartenol content in the roasted nuts did not depend on storage duration. The sterols present in nuts, raw or roasted using either method, transform more during the first 6 months of storage.