The effects of meal size and frequency on equine cecal microbiota are not well documented. We hypothesized that changes in feeding management (including differing meal size and frequency) would alter the equine cecal microbiota. Cecally cannulated horses (n = 6) were utilized in a 3 × 3 Latin square where they received group pasture turnout daily and were stalled overnight in box stalls (3 × 4 m). Treatment diets consisted of Strategy® concentrate and were as follows: A = one meal, 2.72 kg, 6 AM; B = two meals, 1.36 kg/meal, 6 AM and 4 PM; and C = three meals, 0.91 kg/meal, 6 AM, 12 PM, and 4 PM. Treatment periods consisted of 8 days of acclimation followed by 3 days of collection. All horses received ad libitum access to water, a white salt block, and 3 kg of mixed alfalfa/grass hay offered overnight. Cecal samples were sequenced using 16S rRNA gene-based Illumina technology. Data were analyzed using QIIME 1.8.0 and Proc MIXED of SAS. Weighted principal coordinates analysis values indicated that feeding management impacted cecal microbiota composition with horses fed one large meal having different microbial community than those fed three smaller meals throughout the day (P = .028). Furthermore, treatment affected (P < .05) Prevotella, YRC22, Lactobacillus, Streptococcus, Coprococcus, and Phascolarctobacterium. These data demonstrate that feeding a single large bolus meal affects both abundance and composition of the cecal microbiota. Further research is necessary to understand the metabolic and/or health implications related to changes the equine cecal microbiota.