Herbal plants have the potential to reduce the population of metagonic bacteria and protozoa due to the bioactive compound contained in herbal plants. This study aimed to evaluate the effect of herbal plant supplementation on rumen fermentation characteristics, methane (CH4) gas emissions, in vitro nutrient digestibility, and protozoan populations. This study consisted of two stages. Stage I involved determining the potential of herbal plants to increase total gas production (Orskov and McDonald methods) and reduce the protozoan population (Hristov method). Three potential herbs were selected at this stage and used in Stage II as supplements in the palm kernel cake (PKC)-based diet (30% herbal plants + 70% PKC). Proximate and Van Soest analyses were used to determine the chemical composition. In vitro dry matter digestibility (IVDMD), organic matter (IVOMD), and rumen fermentation characteristics were determined using Theodorous method. Conway microdiffusion was used to determine ammonia concentration (NH3). Gas chromatography was used to determine the total and partial volatile fatty acid production. The results of the first stage showed that seven herbal plants (Moringa oleifera, Rhodomyrtus tomentosa, Clerodendron serratum, Curcuma longa Linn., Urena lobata, Uncaria, and Parkia timoriana) significantly differed in terms of total gas production (p < 0.05). Herbal plants can increase gas production and reduce protozoan populations. The highest total gas production was observed using P. timoriana, M. oleifera, and C. longa Linn. Moringa oleifera plants were the most effective in lowering protozoa population. In Stage 2, the supplementation of herbal plants in PKC-based-diet significantly increased IVDMD, that was ranged from 56.72% to 65.77%, IVOMD that was ranged from 52.10% to 59.54%, and NH3, that was ranged from 13.20 mM to 17.91 mM. Volatile fatty acid partial and total gas production potential and CH4 gas emissions were also significantly different from those of the control (p < 0.05). Supplementation of M. oleifera, C. longa Linn., and P. timoriana in ruminant diet effectively increased total gas production, IVDMD percentage, and IVOMD, and reduced CH4 gas emissions and protozoa populations during rumen fermentation.