The aim of this work was to study the effects of microwaves (MW) and hot air (HA) treatments on enzyme activities and quality parameters in wheat germ (WG). Both MW and HA were effective at inactivating lipases. MW treatment inactivated lipases more at lower temperatures (60 and 70 °C) than HA (150–200 °C). Peroxide values, acidity, and fatty acid profiles of WG oil remained unaltered after HA and MW treatments. Loss of α-tocopherol contents was observed following HA treatment, but total tocopherol content remained above 77% baselines values in all treated samples. The main antioxidant mechanism of WG extracts was associated with inactivation of radicals, rather than reducing capacity. MW treatment at 60 and 70 °C enhanced radical scavenging activity, while total polyphenol contents and reducing capacities were negatively affected. Therefore, MW treatment is a promising technology to stabilise WG, retaining quality and antioxidant activity.