Planted cover crops and naturally occurring resident vegetation in orchards and agricultural fields belong to multiple functional groups which differ in traits, growth dynamics, and ability to influence soil health and biology. These different vegetation mixes may influence soil food webs and ecosystems over a growing season as well as regulating nutrient cycling outcomes. This study characterized soil organisms and nutrients as well as physical and chemical indicators of soil health in an almond orchard with three vegetation mixes: winter resident vegetation (dominated by Vicia, Malva, and Hordeum weedy species), and two cover crops mixes, one functionally diverse (brassica, legume, cereals) and one functionally uniform (brassicas), all of which had been implemented for four years. While physical soil health indicators differed seasonally, only biological indicators differed among the vegetation. During the winter and early spring growth period, both cover crop mixes increased microbial biomass nitrogen compared to resident vegetation, while the uniform mix supported greater numbers of nematodes overall, regardless of trophic group. The diverse cover crop mix supported more complex nematode food webs, as measured by the Structure Footprint, while nematode communities overall were primarily influenced by cover crop biomass and microbial biomass nitrogen. Soil nutrients increased after vegetation termination by flail mowing in all treatments, and the resident vegetation had the largest increase in dissolved organic carbon between the Cover and Post-Cover time points. Nematode indicators of food web composition and function decreased after termination, including the Structure Index, Fungal Footprint and Bacterivore Footprint. In contrast, the relative abundance of herbivores increased over time and, at the Post- Cover time point, both the diverse mix and the uniform mix had a higher proportion of root herbivores than resident vegetation, although these were primarily in the genus Tylenchorhynchus and not considered economically damaging. Increased processing of resources through generalist root herbivore nematodes may have been due to nematodes feeding on the cover crops themselves or on almond roots that foraged into soils with more nutrients. These results suggest that cover cropping can influence soil food webs on multiple fronts including root herbivores and predators. Greater knowledge of how cover crops influence soil health and for how long, during a season, will allow for the more efficient use of cover crops in Mediterranean systems.