For >2 years, Japan’s government has been urging the populace to take countermeasures to prevent COVID-19, including mask wearing. We examined whether these preventive behaviors have affected the rate and degree of sensitization against pollen and house dust antigens in patients with allergic rhinitis. We retrospectively surveyed 2565 patients who had undergone allergy blood testing during the period 2015–2021. We subdivided this period into eras based on the COVID-19 pandemic: the pre-COVID (2015–2019, n = 1879) and COVID (2020–2021, n = 686) eras. The positive rates for Japanese cedar and cypress in the 40–59-year-olds and those for house dust in the 20–39-year-olds were significantly reduced in the COVID era versus those in the pre-COVID era. Each group’s mean antigen-specific CAP scores decreased significantly from the 1st to 2nd era: from 1.98 to 1.57 for cedar (p < 0.01), 1.42 to 0.95 for cypress (p < 0.05), and 2.86 to 2.07 for house dust (p < 0.01). Our survey of the patients’ clinical records indicates that 47.5% of the pollinosis patients reported improvement in nasal symptoms after the three seasons of pollen dispersion in the COVID era. Japan’s quarantine policies designed to combat the spread of COVID-19 thus coincide with pivotal measures to alleviate allergic reactions.