Honey is a natural product made by honeybees, its composition depends on factors such as climate, soil and plant source. In this study, the nutritional parameters, phenolic composition, antioxidant activity and antibacterial ability of 30 different types of honey of different botanical and geographical origins in Vietnam were investigated. The study focused on the characterization and evaluation of the influence of plant origin and geographical location on physical–chemical properties and biological activities (antioxidant and antibacterial). The obtained results show that all honey samples meet quality standards according to international standards and Vietnamese standards, except for some exceptions recorded in moisture, 5-hydroxymethylfurfural (HMF) value and ash. These samples were explored for the detection of 13 polyphenols by using high-performance liquid chromatography (HPLC). The classification of honey samples collected from different regions and botanical sources was performed by principal component analysis (PCA), and it was observed that certain phenolic compounds contributed to the identification of honey samples. In addition, the correlation between physicochemical properties, chemical composition and biological activity of most honeys was also first clarified in this study. Overall, our data provide an overview data set and essential results in creating a database on the world honey trait map.