Coffee berry disease ( Colletotrichum kahawae ) causes fruits rots on Arabica coffee leading to harvest losses of around 40%. Using biological molecules may be one way of reducing chemical pesticide use by stimulating natural defence reactions in plants. FEN 560 is a natural product extracted from fenugreek ( Trigonella foenum-greacum ) and its stimulating effect is now recognized on the Vitis vinifera L./ Uncinula necator pathosystem. In order to study its effect on the Coffea arabica / C. kahawae pathosystem, the enzymatic activity of phenylalanine ammonia lyase (PAL), along with caffeine and chlorogenic acid (CGA) concentrations were monitored in the seedling hypocotyls of two varieties of C. arabica with different degrees of susceptibility, contaminated by C. kahawae and treated with FEN 560. After observing symptoms on seedlings, a real FEN 560 effect was seen on the pathosystem. However, it did not seem to stimulate the alkaloid (caffeine) or polyphenol (CGA) biosynthesis pathways. However, the pathogen did trigger synthesis of caffeine and CGA, which therefore seem to be useful markers for studying resistance to coffee berry disease in C. arabica.