The physicochemical and phytochemical analyses of honeys (n = 50) from Sudanese, Sudano-Guinean, and Guinean areas of Benin were investigated. Results showed that dark amber is the dominant color. Moisture content ranged from 15.50% to 23.50%, and 72% of honeys respected the Codex Alimentarius recommendation. pH varied between 2.87 and 6.15, and free acidity ranged from 9.00 to 39.00 meq/kg. Electrical conductivity varied from 0.37 to 1.43 mS/cm. The content in fructose varied from 21.67% to 94.21%, and proline content ranged between 306.31 and 1187.93 mg/kg. All physicochemical characteristics varied with the areas. A negative correlation was found between pH and moisture content (r = -0.55; p < 0.01). A positive correlation was established between pH and conductivity (r = 0.79; p < 0.01) and between proline and color (r = 0.44; p < 0.01). Total phenolic content varied between 55.97 and 224.99 mg GAE/100 g, and flavonoid content ranged between 1.43 and 29.81 mg CAE/100 g. Flavonoid was positively correlated with color (r = 0.78; p < 0.01) and proline (r = 0.47; p < 0.01). Tukey's test revealed differences between total phenolic and flavonoid contents of honeys from five areas (p < 0.01). In general, Sudanese and Sudano-Guinean honeys showed potential toward therapeutic applications because of their high phenolic contents.