The objectives of the present study are to compare the phenolic profiles and biological activities of 15 citrus honey samples from three different locations in Turkey using a chemometric approach. The HPLC‐DAD analysis was used to determine phenolic profiles. Nineteen phenolic compounds were identified. Gallic acid (107.14‐717.04 μg/g) was recorded as the predominant compound. AF (Antalya‐Finike) had the highest antioxidant activity in ABTS•+ (IC50: 18.01±0.69 mg/mL), metal chelating (IC50: 6.20±0.19 mg/mL) and CUPRAC (A0.50: 12.05±0.68 mg/mL) assays, while it revealed the best anti‐inflammatory activity against COX‐2 (17.28±0.22%) and COX‐1 (43.28±0.91%). AM (Antalya‐Manavgat) was the most active in β‐carotene‐linoleic acid (IC50: 10.05±0.19 mg/mL), anti‐urease (38.90±0.69%), anti‐quorum sensing and antimicrobial activities. AKO1 (Adana‐Kozan‐1) in DPPH• (IC50: 34.25±0.81 mg/mL) assay, AKU1 (Antalya‐Kumluca‐1) in tyrosinase inhibition activity (37.73±0.38%) assay, AKU2 (Antalya‐Kumluca‐2) in AChE (10.55±0.63%) and BChE (9.18±0.45%) inhibition activity assays showed the best activity. Chemometric tools were applied to the phenolic compositions and biological properties. PCA and HCA ensured that 15 citrus honey samples were grouped into 3 clusters. The results showed that myricetin, kaempferol, vanillin, protocatechuic acid, rosmarinic acid, rutin, vanillic acid, gallic acid, catechin and p‐hydroxyphenyl acetic acid are phenolic compounds that can be used in the classification of citrus honeys.