Coffee, one of the most popular beverages in the world, contains many bioactive compounds. The aim of this study was a comparative evaluation of the content of bioactive compounds in organic and conventional coffee (Coffea arabica) originating from Brazil during 12 months storage. The content of the polyphenolic compounds was determined using HPLC analysis. The obtained results indicate that organic or conventional production and roasting conditions (light, medium, dark roast) affect the polyphenolic compounds of coffee. The highest content of total polyphenolic compounds was determined in coffees roasted in light and medium roasting conditions. Furthermore, organic coffee beans showed higher content of bioactive compounds (total phenolic, phenolic acids and flavonoids) than conventional coffee beans. During 12 months storage a decrease in polyphenolic compounds is observed and it is connected with the degradation of chlorogenic acid, which influences total bioactivity. Moreover, the highest caffeine content was observed in light and medium roasted coffee and after storage an increase in caffeine content was observed only in organic coffee beans.