Physicochemical characteristics, main minerals, and antioxidant activity were determined for Palestinian honey samples belonging to different floral and geographical origins. The features of the analyzed samples were within the established international standards for honey quality control. One clear exception was the hydroxymethylfurfural (HMF) of the Ziziphus sample purchased from the Jericho region, which is the lowest city in the word characterized by a hot desert climate. The observed HMF value was 81.86 ± 2.64 mg/kg being two folds the maximum allowed in honey samples (40 mg/kg). As a second objective of the present work, the parameters were divided into two groups with different discriminatory power. The assessed physicochemical parameters, and the antioxidant activities, specific to the botanical origin discrimination, were used to run the first PCA. A strong correlation could be seen between the bioactive compounds and the antioxidant activities despite the geographical origin of the samples. Thyme and Ziziphus samples were the best samples, while citrus sample presented the lowest activity. Regarding the geographical discrimination, Ash and mineral contents in addition to the electrical conductivity were used. The output PCA conserved high represent ability of the data in the two‐first components being 82.72% and 9.60%. A little discrimination between the samples produced in the north and those produced in the south of the country, but it was not perfect. The intervention of the botanical variability could be the reason.