Iran, a leading honey-producing country, faces challenges in honey exports. This study aimed to evaluate the melissopalynological and physicochemical characteristics of local honeys belonging to Iranian flora, and compare them with Iranian commercial honeys. For this purpose, seven local honey samples were collected from Iran's renowned floristic regions, alongside seven commercial multi-floral honeys from a supermarket. Moisture content (MC), total solids (TS), pH, free acidity (FA), ash, electrical conductivity (EC), sugar profile, hydroxymethyl furfural (HMF), diastase number (DN), and proline were assessed. The sugar profile was analyzed by high-performance liquid chromatography with a refractive index detector (HPLC-RID). Pollen analysis classified local honeys as multi-floral. The results revealed that MC, TS, pH, FA, ash, and EC values in both local and commercial samples conformed to approved standards (Codex Alimentarius and European Union). Two local and one commercial sample exclusively satisfied the sucrose standard level. Of the local honeys, two samples complied with HMF standard, while five fulfilled DN criterion, and four had proline values within acceptable ranges. Conversely, HMF (56.32–228.11 mg/kg), DN (3.13–7.22 Schade units/g), and proline (109.84–173.86 mg/kg) levels in all commercial samples failed to meet the standard. A significant correlation was found between ash and EC (r = 0.915, p < 0.01) in local honeys, whereas no strong correlation (r = 0.299) existed in commercial samples. Hierarchical cluster analysis confirmed that Iranian honeys lacked clustering by botanical origin, possibly due to extensive sugar adulteration or thermal treatment. Overall, study findings confirmed the significantly inferior quality of Iranian commercial honeys compared to local varieties, albeit some local samples also exhibited quality concerns. Accordingly, it is recommended that regulatory bodies provide periodic training for beekeepers and establish monitoring programs to enhance honey quality, thereby boosting Iran's share in the global honey export market.