Five types of honey (multifloral, sunflower, linden, rapeseed, and acacia), from Southern Romania, were classified using chemometrics methods coupled with IR spectroscopy. The botanical origin’s effect on the physicochemical characteristics of honey was studied to highlight the most valuable plant source of honey. Except for antioxidant activity, the moisture, ash, electrical conductivity (EC), pH, free acidity (FA), total sugar content (TSC), hydroxymethylfurfural (HMF), total phenolic (TPC), tannin (TTC), and flavonoid content (TFC) were significantly influenced by the botanical origin of the honey. The results showed that sunflower honey had the highest moisture (15.53%), free acidity (16.67 mEq kg−1), electrical conductivity (483.92 µS cm−1), phenolics (167.59 mg GAE 100 g−1), and flavonoids (19.00 mg CE 100 g−1), whereas multifloral honey presented the highest total sugar content (69.64 g Glu 100 g−1). The highest HMF content was found in linden honey (33.94 mg kg−1). The HMF contents of all tested honey were within the standard recommended limit, and they confirmed that the tested honey was free of any heat treatment. All five types of tested honey presented a safe moisture content for storage and consumption (12.21–18.74%). The honey′s free acidity was in the range of 4.00 to 25.00 mEq kg−1; this indicated the freshness of the samples and the absence of any fermentation processes in the tested honey. Honey with a total sugar content over 60% (except for linden honey, with 58.05 g glucose 100 g−1) showed the characteristic of nectar-derived honey. The elevated antioxidant activity of honey was correlated with its high moisture, flavonoids, and HMF, whereas the tannins and HMF were positively correlated with ash and electrical conductivity. The higher content of phenolics, flavonoids, and tannins was correlated with higher free acidity. The chemometric method, coupled with ATR-FTIR spectra, revealed a clear separation between linden honey from acacia, multifloral, and sunflower honey.