Five honeys were treated with static magnetic field (induction 450–480 mT or 130–150 mT) and alternating magnetic field (frequency 50 Hz, induction 30 mT) for 11 h to study the changes of diastase no., content of 5-hydroxymethylfurfural (5-HMF) and attenuated total reflection Fourier transform IR spectra. The mean 5-HMF content (2.41 mg/kg) increased by up to 50% after the treatment. The mean diastase no. (67.59) was changed and the enzymatic activity in honey was also modified. The FTIR analysis showed the structural changes in the honey after the treatment.