The paper aimed to compare the quality of rapeseed and honeydew honey powders, obtained by two methods of spray drying—traditional at a high temperature (inlet air 180 °C) and innovative low-temperature spray drying with the use of dehumidified air as a drying medium (inlet air 75 °C). Total polyphenol content, antioxidant activity, and the content and types of aromatic compounds were determined. In addition, Fourier-transform infrared spectroscopy (FTIR) coupled with chemometrics analyses was done. Powders obtained by the low-temperature spray drying method (with dehumidified air) were characterized by a higher content of polyphenols, antioxidant activity, and aromatic compounds, compared to powders obtained by the traditional method. Honeydew honey compared to rapeseed honey was characterized by a higher content of polyphenols, antioxidant activity, and composition of aromatic compounds. The results proved that the production method had a higher impact on the final properties of powders than the type of honey.