Imbalanced microbiota related to intestinal leakage is an emerging health problem in commercial broilers associated with partial loss of gut function and reduction in growth performance. Salinomycin is an ionophore coccidiostat with antibiotic effect, which is used as additive in broiler diets to control enteric diseases and improve performance. Due to the growing concern of the development of bacterial antibiotic resistance, ionophores are expected to be banned, within the EU, as feed additives in the near future. Butyrate with multiple beneficial effects on growth performance and pathogen control in broilers has been introduced as a promising alternative. In this study, the ability of a coated butyrate product to alleviate intestinal imbalance was compared to that of salinomycin after enteric challenge. Compared to butyrate and non-supplemented control, salinomycin increased potentially beneficial Ruminococcaceae and reduced potentially pathogenic Enterobacteriaceae, and counts of Lactobacillus salivarius and Clostridium perfringens. Further, salinomycin improved broiler performance. Dietary inclusion of coated butyrate had only limited effects on the composition of the broiler microbiota. Whether improved growth and feed utilization in the salinomycin-supplemented animals can be explained by suppression of C. perfringens and L. salivarius and enrichment of butyrate- and lactic acid-producing bacteria (Ruminococcaceae and Lactobacillaceae) needs further verification.