<p>Nowadays, the trend related to the production of functional food with prolonged shelf-life and improved properties is observed. In this view, the thermal treatment method frequently implemented for preservation of drinks can impede food quality by deterioration of its physical parameters besides reaching the aim of prolongation of the shelf-life. In this study, we proposed a method for obtaining honey-based solutions of the specified physicochemical, nutritional, and microbiological properties by employing the pulse-modulated radio-frequency atmospheric pressure glow discharge (pm-rf-APGD) plasma treatment. It was found that the subjection of the honey-based solutions to pm-rf-APGD lowers the pH by an average 1.5 times and increases the conductivity at least twice. Furthermore, the concentrations of polyphenolic compounds determined in honey solutions increased on average from around 20 to 201 mg L^− 1 post pm-rf-APGD exposure. Referring to the elements detected in the studied honey-based solutions, no statistically significant deviations in the contents of Al, Ba, Ca, Cu, Fe, K, Mg, Mn, Na, Sr, and Zn were identified. The honey-based solutions that were treated with pm-rf-APGD exhibited a significantly lower microbial load (~ 0 CFU mL^− 1) compared to the untreated controls (&gt; 3000 CFU mL^− 1) over a 15-day storage period. Based on the performed studies, it was concluded that the pm-rf-APGD exposure has a positive impact on the physico-chemical, nutritional and microbiological properties of the honey-based solutions.</p> Graphical Abstract <p></p>