Treatments to control Varroa destructor using Apilife VAR® and alternatively by using homemade preparations of thymol were carried out on professional honeybee (Apis mellifera L.) hives in Spain with the aim to evaluate the presence of residues of essential oils that may contribute to honey’s undesirable flavor and odor. Using HRGC-FID/MS after Apilife VAR® treatment, thymol was detected in 89% of the samples (mean, 0.78 μg/g), menthol in 15% (mean, 0.27 μg/g), and camphor and eucalyptol were not found (< LOQ). In homemade preparations, thymol was detected in the 86% of the samples analyzed after treatment with thymol solution in ethanol (mean, 1.18 µg/g), and in the 90% of the samples (mean, 0.95 µg/g) after treatment with thymol solution in olive oil. Only in 11% of the samples the concentration of thymol exceeded the taste threshold (1.20 μg/g), with negative effect on sensorial quality of the honey. Thymol residues in honey are clearly below the recommended limit and furthermore, these compounds quickly decrease due to his volatility, thus there cannot be any food safety risk for the consumer.