An experiment was conducted to study the effects of microbial phytase (PHY), citric acid (CA), and Cu proteinate supplementation in broiler chickens (13 to 42 d of age) fed a low available P diet (0.25%) on ileal and carcass microbiota of broiler chickens. A factorial arrangement of treatments (2 x 2 x 2) was used to evaluate 2 levels of PHY (0 and 750 units/kg), Cu (0 and 250 ppm), and CA (0 and 3%). A total of 10,080 birds were placed into 48 floor pens (210 birds per pen) and fed a commercial broiler starter diet until 13 d of age. Addition of 750 phytase units of PHY significantly reduced the log(10) counts for total anaerobic bacteria, Escherichia coli, and coliform bacteria in the ileal digesta of chicks (0.28, 0.22, and 0.59 log(10), respectively). Copper supplementation had no effect on pH or microbial counts in the ileal contents. However, Cu supplementation significantly increased the populations of Staphylococcus (P < 0.01) and lactic acid bacteria (P < 0.001) on the carcass. Citric acid supplementation significantly decreased ileal coliform contents (P < 0.05) but increased the populations of Staphylococcus (P < 0.05), Campylobacter (P < 0.05), and lactic acid bacteria (P < 0.001) on the carcasses. In conclusion, neither 3% CA nor Cu supplementation of broiler diets reduced the numbers of pathogenic bacteria in the ileum or on the carcass, but PHY supplementation might effectively decrease ileal pathogenic bacterial populations and beneficially affect gut health. Future research on how PHY affects the intestinal bacteria of a bird might provide new approaches for microbial mitigation in poultry.