The aim of this study was to evaluate the effect of ultrasound treatment for preventing honey crystallization on the physicochemical and microbiological properties of unifloral honey and polyfloral honey. Honey samples without any treatment were used as a control group for comparison. The effect of applying ultrasound treatment was evaluated by studying over time the tendency of crystallization, the rheological properties of honey and chemical and microbiological properties. The parameters analyzed for the two groups of samples (treated and untreated with ultrasound), which did not vary or had small variations during the research were water content, acidity, water activity, glucose, fructose, sucrose, glucose/water ratio, glucose/fructose ratio. The crystallization process was installed in the control samples from the first month of the study, and much later in the treated samples. The color of the untreated samples varied considerably, and the color of the treated ones remained stable or slightly varied. For the control samples, the smallest variation in hydroxymethylfurfural (HMF) concentration was in raspberry honey (5%), and the most significant variation was in honeydew honey (30%). For the treated samples, the largest variation of this parameter was found in tillia honey (127%), and the smallest variation was in rapeseed honey (26%). The microbiological quality was higher for the treated samples. In the ultrasound-treated samples of acacia honey, honeydew honey and grassland honey, yeasts, molds or standard plate counts (SPCs) were undetectable. For control samples, SPC values were <10–50 cfu/g. Ultrasound-treated samples maintained their SPC parameter levels or were thus reduced (<10–20 cfu/g). Yeasts and molds were undetectable or had value between <10 and 10 cfu/g. The yeasts and the molds ranged in the control samples between <10 and 40 cfu/g.