Many problems in poultry production are caused by a combination of interrelated factors such as management, stress, nutrition, and exposure to pathogens. Saprophagous flies that develop in poultry manure are a potential route of pathogen transmission. Besides being a nuisance, defecation and regurgitation of flies soil equipment and structures and can reduce light levels of lighting fixtures. These effects clearly affect management and may contribute to reductions in poultry egg production, health, and welfare. Many essential oils or their main components have bioactive effects such as natural repellents and insecticides, antioxidants, anticholesterolemics, and antimicrobials. This study evaluated if supplementing quail feed with thymol or isoeugenol as functional food could alter the production of flies from manure. Dropping samples deposited by quail fed with a supplementation of 2,000 mg of thymol or isoeugenol per kg of feed or no supplement (control) were collected. Each sample was incubated inside an emergence cage that was inspected daily to collect emerging adult flies. Fewer flies emerged from droppings of quail fed a thymol-supplemented diet (P = 0.01) and there was a tendency to a lower emergence from droppings of isoeugenol-fed quail (P = 0.09). The number of positive containers for Musca domestica was smaller from quail droppings of thymol- (P = 0.02) or isoeugenol- (P = 0.01) supplemented feed than from the control counterparts, suggesting an oviposition repellent effect. Supplementing quail feed with thymol or isoeugenol has an overall moderate effect against flies, reducing M. domestica emergence.