Coffee berry disease (CBD) caused by Colletotrichum kahawae is a major constraint of Arabica coffee production in Africa. CBD-related losses in Cameroon might be estimated to reach up to 80%. The objectives of this study were to compare the efficacy of fungicides on disease incidence at the level of coffee branches and to determine the impact of fungicide on coffee yield. Data via experimental design were conducted at Kouoptamo; West region of Cameroun. Coffee trees were treated for two successive years (2016–2017) with Propiconazole, Difenoconazole, Azoxystrobin and Chlorothalonil/Carbendazim at frequencies of 21 and 28 days at the rate of 4 and 5 annual applications depending on the fungicide. The lower proportion of diseased branches (Estimated Marginal Mean, EMM 16%) and infected berries on the diseased branches (EMM, 7%) was observed on plants treated with Azoxystrobin compared to control (EMM, 55 and 21%, respectively). Branches at the lower level of the tree were more likely to have infected berries than branches in the middle or the upper branches (EMM 19% against 16 and 14%) regardless of the treatment. The yield of Azoxystrobin-treated coffee trees was twice as high as those of the control over the two years of experimentation. This is the first report of the use of Azoxystrobin against CBD and can open a new insight into optimizing effective control of CBD in Arabica coffee plantations.