The aim was to investigate the impact of an automatic in ovo injection of the raffinose family oligosaccharides (RFO) extracted from the seeds of Lupinus luteus L, on the chicken performance and resistance in a production environment. At day 12 of incubation, a total of 57,900 eggs (Ross 308) were divided into two groups: 1/ Control, injected with 0.9% NaCl and 2/ RFO group, injected with 1.9 mg/egg of the lupin seed extract, dissolved in 0.2 mL NaCl. The performance parameters, biochemical indices (lipid profile, hepatic parameters), gut histomorphology and duodenum structure, oxidative stability of the meat and microbiological counts of the major commensal microbiota species were analyzed. Mortality, body weight, and feed conversion ratio (FCR) were not affected. By day 42, several health indices were improved with RFO and were reflected in a beneficial lipid blood profile, increased villi surface and better combating opportunistic pathogens through reduction of Clostridia and decreased coccidia counts. The RFO increased meat oxidation, but only at the beginning of the storage. The RFO sourced from local legumes can be considered a promising prebiotic for broiler chickens. In ovo delivery of prebiotics and/or synbiotics should be further optimized as an important strategy for the earliest possible modulation of chicken resistance.