A 2 × 2 factorial experiment was conducted to assess the effects of presence or absence of rumen protozoa and of dietary coconut oil distillate (COD) supplementation on rumen fermentation characteristics, digesta kinetics and methane production in Brahman heifers. Twelve Brahman heifers were selected to defaunate, with 6 being subsequently refaunated. After defaunation and refaunation, heifers were randomly allocated to COD supplement or no supplement treatments while fed an oaten chaff-based diet. Methane production (MP; 94.17 v 104.72 g CH4 /d) and methane yield [MY; 19.45 v 21.64 g CH4 /kg dry matter intake (DMI)] were reduced in defaunated heifers compared with refaunated heifers when measured at 5 weeks after refaunation treatment (p < 0.01). Supplement of COD similarly reduced MP and MY (89.36 v 109.53 g/d and 18.46 v 22.63 g/kg DMI, respectively; p < 0.01), and there were no significant interactions of defaunation and COD effects on rumen fermentation or methane emissions. Concentration of total volatile fatty acid (VFA) and molar proportions of acetate, propionate and butyrate was not affected by defaunation or by COD. Microbial crude protein (MCP; g/d) outflow was increased by defaunation (p < 0.01) in the absence of COD but was unaffected by defaunation in COD-supplemented heifers. There was a tendency towards a greater average daily gain (ADG) in defaunated heifers (p = 0.09), but COD did not increase ADG (p > 0.05). The results confirmed that defaunation and COD independently reduced enteric MP even though the reduced emissions were achieved without altering rumen fermentation VFA levels or gut digesta kinetics.