Campylobacter jejuni, a major enteric pathogen and a natural resident in the poultry gut, causes gastrointestinal illness followed by severe post-infection complications, including Guillain-Barré syndrome, reactive arthritis, myocarditis, and ulcerative colitis in humans. Risk assessment studies have projected a 30-fold reduction in human campylobacteriosis cases with only a 100-fold reduction in the number of C. jejuni colonizing the poultry gut. Current commercial poultry production practices involve use of antibiotic growth promoters (AGP); modulation of gut microbiota with AGPs for food safety and enhanced performance in poultry can be justified until acquisition of antibiotic resistance in zoonoses through inter-bacterial transfer of antibiotic resistance genes (ARGs) in a complex microbial community is considered. As an alternative, natural phenolics extracted from by-products of berry juice industry, with antimicrobial, anti-inflammatory, anticarcinogenic, antioxidant and vasodilatory activities, demonstrate promising prospects. In this study, we adopted mass-spectrometry, microbiological, phylogenetic, and metagenomic approaches to evaluate bioactive phenolic extracts (BPE) from blueberry (Vaccinium corymbosum) and blackberry (Rubus fruticosus) pomaces as AGP alternative. We detected that major phenolics in BPE included, but were not limited to, apigenin, catechol, chlorogenic acid, cinnamic acid, coumarin, ellagic acid, eugenols, flavan, gallic acid, gingerol, glucosides, glucuronides, myricetin, phenols, quercetin, quinones, rhamnosides, stilbenol, tannins, triamcinolone, and xanthine. BPE reduced C. jejuni growth and motility in vitro, resulting in lower adherence and invasiveness to chicken fibroblast cells. Anti-inflammatory effects of BPE significantly reduced the expression of pro-inflammatory cytokine genes in chick macrophage cell line ex vivo. Furthermore, BPE reduced the colonization of C. jejuni in broiler cecum by 1 to 5 logs while increasing broiler weight by 6% compared to 9.5% with commercial AGPs. Metagenomic analysis of broiler gut indicated that BPE caused an AGP-like pattern in bacterial communities with a comparative increase of Firmicutes and a concomitant reduction of Bacteroidetes in broiler ceca. AGP supplementation clearly caused phage induction and a richer resistome profile in the cecal microbiome compared to BPE. Functional characterization of cecal microbiomes revealed a significant variation in the abundance of genes involved in energy and carbohydrate metabolism. Our findings established a baseline upon which mechanisms of plant based antimicrobial performance-enhancers in regulation of animal growth can be investigated.