This study presents a detailed characterization of 27 honey samples from the Tara Mountain region in Serbia using different comprehensive techniques and methods. The types of the honey samples were defined as monofloral (4 samples), honeydew (5 samples) and polyfloral (18 samples) honey based on determined polyphenol content, antioxidant activity, electrical conductivity and melissopalynological analyses. Physicochemical parameters such as pH (4.13–4.94), diastase activity (24.20–41.70 DN), acidity (14.60–29.70 meq/kg), content of 5-(hydroxymethyl)furfural (in range below 5, up to 16.90 mg/kg), sucrose (0.20–3.90 g/100 g), and moisture content (15.01–19.23%) confirmed the required quality of the honey samples. Sensory analysis revealed honey characteristics favorable to consumers. Analyses of 19 phenolic compounds using ultra-high-performance liquid chromatography with a diode-array detection and triple quadrupole mass spectrometry (UHPLC-DAD-MS/MS) revealed six phenolic acids and 13 other compounds from the group of flavonoids and their glycosides. In all the samples the highest content was determined for p-coumaric acid, followed by caffeic acid and pinocembrin. Besides total phenolic content and radical scavenging activity, antimicrobial activity was also examined. Most honey samples showed bactericidal activity against Staphylococcus aureus and bacteriostatic activity against Escherichia coli, while none of the honey samples inhibited the growth of Candida albicans. Chemometric analyses were applied for an in-depth study of the results to further evaluate the characteristics of the honey samples studied. Principal component analysis (PCA) was used for assessing the differences in physicochemical parameters, polyphenols content and antioxidant capacity between honey samples. The unrooted cluster tree was used to group the samples based on the melissopalynological analyses.