This work aimed at the chemical and structural characterization of powders obtained from chestnut flower honey (HFCh) and honey with Inca berry (HBlu). Honey powders were obtained by spray drying technique at low temperature (80/50 °C) with dehumidified air. Maltodextrin (DE 15) was used as a covering agent. The isolation and evaluation of phenolic compounds and sugars were done by gas chromatography–mass spectrometry analysis. Scanning electron microscopy, Fourier-transform infrared (FTIR) spectroscopy, and X-ray diffraction were performed to determine the morphology of the studied honey powders. The obtained results showed that the content of simple sugars amounted to 72.4 and 90.2 g × 100 g−1in HFCh and HBlu, respectively. Glucose was found to be the dominant sugar with a concentration of 41.3 and 51.6 g × 100 g−1in HFCh and HBlu, respectively. 3-Phenyllactic acid and ferulic acid were most frequently found in HFCh powder, whereas m-coumaric acid, benzoic acid, and cinnamic acid were the most common in HBlu powder. The largest changes in the FTIR spectra occurred in the following range of wavenumbers: 3335, 1640, and below 930 cm−1. The X-ray diffraction profiles revealed wide peaks, suggesting that both honey powders are amorphous and are characterized by a short-range order only.