Antimicrobial resistance demands the development of therapeutic alternatives such as prebiotics, probiotics, and nutraceuticals. The aim of this study was to assess the antimicrobial proprieties of the nutraceutical fermented defatted “alperujo”, derived from olive oil production, in a laying hen farm (n = 122,250) endemic with avian intestinal spirochetosis (Brachyspira spp.). Part of the batch (n = 1440) was divided into six groups of 240 hens each that included 80 or 108-week-old laying hens, supplemented with 0%, 2%, or 6% fermented defatted ‘alperujo’ for a month. At the end of the experiment, eight hens from each group were autopsied and cecal content was subjected to (i) Brachyspira culture and species identification by PCRs, and (ii) direct DNA extraction and Brachyspira qPCR. Furthermore, the ceca were processed for histopathology. Microbiological isolation revealed B. pilosicoli and B. hyodysenteriae co-infection in all groups. The 80-week-old hen group 2% supplemented showed a reduction in the cecal Brachyspira content (qPCR) compared with non-supplemented hens. Cecal histopathology showed a diffuse mild infiltration of lymphocytes, plasma cells, and heterophils; and hyperplasia of the gut-associated lymphoid tissue hyperplasia which decreased in severity in 80-week-old supplemented hens. The reduction in Brachyspira colonization and the severity of the lesions observed in supplemented hens highlights a potential protective function against avian intestinal spirochetosis.