Abstract Livestock has a significant contribution to methane emission as a portion of their ingested energy, which is wasted in the form of methane (2–15%), and ammonia (75–95%). Microbial fermentation in ruminants results in the loss of energy in methanogenesis and protein via ammonia nitrogen excretion, causing a decline in feed efficiency and acting as environmental pollutants. Antibiotics were used to reduce these losses in the rumen, but this approach was restricted in animal products. Some plants or their bioactive extracts/metabolites such as organo-sulphur compounds, saponins, essential oils, flavonoids, and tannins exhibited the potential to limit the methanogenesis by altering the rumen microflora. Plant extracts, including clove (Syzygium aromaticum) bud oil and clove extracts, were used as feed additives to manipulate rumen fermentation. Clove oil interacts with bacterial cells and inhibits the growth multiplication of methanogenic and deaminating bacteria. This results in a reduction in ammonia, nitrogen, methane, acetate concentration, and high propionate and butyrate concentrations. Eugenol is one of the bioactive constituents in clove that manipulate rumen fermentation by increasing propionate production, decrease acetate and methane production, and alter the proteolysis pattern, peptidolysis, and amino acid deamination in the rumen. The current review reports on using of clove phytochemicals and extracts in manipulating rumen fermentation to inhibit methanogenesis and energy loss as well as ammonia–nitrogen waste.