Honey is a natural food product hypothesized to have significant health-beneficial value. The results of recent studies indicate that the biological activity of honey can also be ascribed to phenolic compounds and their antioxidant activity. The aims of this study were: To determine the phenolic profiles of several varieties of Polish honey and their correlation with various factors influencing the quality of honey, plus to verify the impact of production method (organic/conventional) and the pollen content on these profiles. In total, 11 organic and 11 conventional honey samples from Poland were investigated. The botanical origin of the samples was identified through melissopalynological analysis, whereas individual phenolic compounds were determined by the LC/MS analysis. The Folin–Ciocalteau assay was used for the determination of the total phenolic content (TPC). Moreover, the CIE L*a*b* color values were measured and matched with the above-mentioned parameters. The results of the study contribute to the discussion on the health benefits of organic farming. It was found that chrysin may act as a potential indicator compound. The study confirms the existence of the link between TPC and color, and it shows that there is a correlation between pinocembrin and galangin, two compounds that are reported to ameliorate insulin resistance.