Specialty coffee, according to Specialty Coffee Association of America (SCAA) standards, is coffee which has been standardized from the coffee plantation process until its delivery to the consumer, in compliance with all quality standards, to highlight the characteristics of the beverage. With increasing coffee consumption, more attention is focused not only on the flavour and texture of the drink, but also on the impact of coffee on health. The beneficial effects of coffee on human health are mainly based on a wide range of biologically active components. The coffee composition of the biologically active compounds and flavour compounds are influenced differently by almost all technological processes. The aim of this review was to summarize recent scientific developments about composition of aroma, flavour and biologically active compounds in specialty coffee and evaluate the best possibilities to balance health promoting and flavour attributes. Specialty coffee mainly focuses on fruity, floral, sweet and acidic notes in coffee, which are opposite to phenolic compound aroma characteristics during roasting process. In conclusion, roasting temperature significantly influences all biologically active compounds and important aroma, flavour volatiles in coffee. All compound concentration, except coffee melanoidins, decreases during roasting process. Light-medium roast level could provide stability among floral, fruity aroma, flavour notes and biologically active compounds (phenolic compounds and coffee melanoidins) in coffee.