The rumen constitutes a specialized ecosystem composed of a dense and complex mixture of anaerobic bacteria, archaea, protozoa, fungi and phages, that interact closely in the degradation and fermentation of complex plant material into volatile fatty acids (VFAs), utilized for host energy metabolism, and methane gas. The metabolic functions carried out by the rumen microbiome are of scientific and industrial interest, as it contributes to feed efficiency and production of an important human food source (meat and dairy), but additionally contributes significantly to global methane emissions. Therefore, extensive efforts are needed to mitigate enteric methane emissions from ruminant animals without compromising livestock production. While the protozoal populations in the rumen microbiome can comprise up to 50% of the microbial biomass, their biological and metabolic features remain largely unsettled. Advances in culture-independent “meta-omics” approaches continue to increase our understanding of microbiomes, and by integrating multiple culture-independent meta-omics techniques, we can obtain a detailed real-time and in situ molecular portrait of which organisms occupy specific metabolic niches. By resolving (meta)genome-centric metaproteome datasets from rumen fluid samples originating from dairy cows and goats fed diets supplemented with different lipid sources, we explore protozoal function in the rumen microbiome. We specifically leveraged these data to investigate their active metabolic genes and pathways that are responsible for polysaccharide digestion, generation of hydrogen and production of VFAs. Our results illustrate the significant metabolic influence these under-explored eukaryotic populations have in the rumen, towards both fiber and hydrogen metabolism.