The grazing of Zebu cattle in poor-quality tropical pastures during the dry season has an increased environmental impact and cost of production. The use of condensed tannins (CT) as a natural feed additive to modulate ruminal archaea can mitigate the methane emissions from cattle in tropical systems. We investigated the effects of CT on in vivo methane emissions and rumen microbiota ecology in beef cattle. Batch experiments were also conducted to evaluate the impact of dietary CT on the biogas production from beef cattle manure. Six adult rumen-cannulated Nellore cattle were used in a double 3 × 3 Latin square design. Treatments consisted of three diets containing either a 0%, 1.25% or 2.5% CT additive from Acacia mimosa extract. The experimental period consisted of 63 days, and methane production was measured using the sulfur hexafluoride (SF) technique from Day 16 to 21 of each feeding period. Adding Acacia extract to the diets reduced daily methane emissions per animal. Methane suppression occurred more by reduction of intake than by the direct effect on methanogenic archaea. We verified that CT directly suppresses archaea rumen communities and increases total rumen bacteria. Our study indicates that CT benefit rumen Fibrobactersuccinogenes and Ruminoccous flavefaciens populations and have no negative effect on biogas production from cattle manure. Acacia extract as a feed additive has promising potential as part of an overall nutritional strategy to reduce the methanogenesis from Zebu beef cattle in tropical systems.