•Fatty acids profile in cocoa beans and chocolates with different geographical origin and processing conditions.
•Differences in FAs profile were mainly due in all samples to the geographical origin effect.
•Fifteen FA were identified in cocoa and chocolates samples studied.
•For all samples, C16:0, C18:0, C18:1 and C18:2 were quantitatively the most important FAs.
•Ecuadorian chocolates were those with healthier FAs profile.