Because of the economic importance of fruit flies throughout the world, increased knowledge of alternative hosts of these pests is essential for integrated pest management in economically valuable fruit crops grown in regions where other host plant species such as coffee are also commonly cultivated. Therefore, the objective of this study was to evaluate the suitability of the cultivated coffee species Coffea arabica L. and Coffea canephora Pierre ex A. Froehner as hosts of fruit fly species in the state of Espírito Santo, Brazil, where both coffee species are widely grown in close proximity to a variety of economically valuable, and fruit fly susceptible, commercial fruit crops. Mature fruits of both coffee species were collected from 681 farms in 54 municipalities of Espírito Santo to identify the fruit fly species infesting coffee fruits and determine fruit fly infestation levels. Field and laboratory experiments were also conducted to study the relationships between coffee species and fruit fly infestation and development. Field infestation of coffee fruits by fruit flies was higher in C. arabica than in C. canephora (‘Conilon’). A total of 136.7 fruit fly pupae per kg of C. arabica fruits were found, in comparison to 5.4 pupae per kg of C. canephora fruits, and 97.1% of the adult fruit flies reared from coffee fruits emerged from C. arabica fruits. Ceratitis capitata (Wied.) and Anastrepha fraterculus (Wied.) were the most common fruit fly species associated with fruits of both coffee species. The quantity of C. capitata reared from C. arabica fruits (55.2 adults kg−1) was 15.3 times higher than the quantity reared from C. canephora fruits. Coffea arabica was also a much better host for A. fraterculus than C. canephora based on the number of adults reared from fruits. Results of this study indicate that C. arabica is a potential reservoir host of fruit flies, and therefore may play a significant role in fruit fly pest survival when preferred host fruits are lacking in winter months. This is the first study that compares the two major cultivated coffee species as potential hosts and sources of fruit flies, and indicates that integrated pest management (IPM) should be utilized to inhibit dispersal of fruit flies from C. arabica to nearby areas where commercial fruit crops are grown.