The effect of typical domestic microwave heating (0–15 min, at 800 W) on the thermal degradation of unflavored and flavored olive oils' minor bioactive compounds and related antioxidant activity was studied. Olive oils from cv. Arbequina were flavored with lemon verbena essential oil (0%, 0.2% and 0.4%, w/w) leading to a linear increase of total phenols (112–160 mg gallic acid kg−1 oil, R-Pearson = +0.9870), total carotenoids (2.19–2.56 mg lutein kg−1 oil, R-Pearson = +0.9611), and, to a less extent, of chlorophyll (2.32–3.19 mg pheophytin kg−1 oil, R-Pearson = +0.8238). However, no such linear trend was observed for the oxidative stability (6.5–7.8 h) or the radical scavenging activity (inhibition rates: 40%–43%). The contents of total phenols, total carotenoids, and chlorophyll decreased with the rise of the microwave heating time, following their thermal degradation, a second-order kinetic model (0.8784 ≤ R-Pearson ≤ 0.9926). The essential oil addition did not influence the estimated second-order rate reaction constants of total phenols (0.00070–0.00072 kg oil min−1 mg−1 gallic acid)and total carotenoids (0.14–0.17 kg oil min−1 mg−1 lutein), with a broader variation observed for chlorophyll (0.014–0.022 kg oil min−1 mg−1 pheophytin). Globally, total carotenoids degraded faster than total phenols and chlorophyll (half-life of 2.3–3.4, 8.8–12.8, and 14.5–30.8 min, respectively). Moreover, except for chlorophyll, the half-life of total phenols and carotenoids linearly decreased with the essential oil addition (R-Pearson: −0.9999 and −0.9421, respectively), showing that flavoring did not have a protective effect against degradation when subjected to a microwave heating.