Fasciolosis is a zoonotic food- and waterborne infection related to great economic losses on ruminant production. In order to determine the prevalence of bovine liver condemnations due to fasciolosis in an abattoir at the Central Andes of Peru, we evaluated the records of an authorized slaughterhouse in Huancayo, at 3300 m above sea level, over 16 months. Subsequently, the average weights of condemned viscera and carcasses were also estimated to determine the direct and indirect economic losses. Fasciolosis was the main cause of liver condemnation, with a prevalence of 55.72% (3926/7046; CI 95%: 56.88–54.56%). The livers infected were more than double the amount of livers supplied to markets in this period. Although the average price of liver in the Peruvian Andes is very cheap, approximately 16.45 tons of livers were destroyed, estimating a direct economic loss of US$ 35,080 (CI 95%: US$ 29,178–40,938). The indirect loss due to decreased body weight gain (calculated using 10% of the average weight of a healthy animal carcass) was estimated at US$ 354,570 (CI 95%: US$ 387,908–US$ 321,227). Fasciolosis is an important zoonotic disease that threatens food security in the Andean region, with major repercussions on the income of the livestock industry and the availability of cheap protein sources.