Honey bee viruses in combination with varroa mite are very damaging for honey bee colonies worldwide. There are no effective methods to control the viral load in honey bee colonies except regular and effective control of mites. Integrated Pest Management strategies are required to effectively control mites with veterinary medicines based on organic compounds. We evaluated the effect of two brood interruption techniques, queen caging (QC) and trapping comb (TC), followed by an oxalic acid treatment, on the mite fall, colony strength, and viral load of Deformed Wing Virus (DWV) and Acute Bee Paralysis Virus (ABPV). In this paper, we report the data obtained in two experimental sites, in Slovenia and Italy, in terms of the varroacide efficacy, colony strength, and viral load. The number of adult bees after the adoption of the two techniques showed similar decreasing trends in both locations. The viral load of Acute Bee Paralysis Virus did not show any significant reduction after 25 days, reported as the number of Real-Time PCR cycles needed to detect the virus. The viral load of DWV also did not show a significant reduction after 25 days. The acaricidal efficacy of the applied protocols was high in both experimental groups and in both apiaries. Both the queen caging and trapping comb techniques, followed by an oxalic acid treatment, can be considered effective varroa treatment strategies, but further studies should be carried out to evaluate the long-term effects on viral loads to plan the Integrated Pest Management strategy with the right timing before wintering.