Entomopathogenic nematodes (EPNs) are biological control agents distributed worldwide in natural and agricultural soils. Recent evidence supports the hypothesis that stable rhizospheres of perennial crops can favor the occurrence of EPNs. However, different agricultural management practices can modulate their natural distribution in agroecosystems, hence should be considered in conservation biological control programs to support as high as possible native EPN populations. Cultivated olive (Olea europaea subsp. europaea), originally from the Mediterranean Basin, is a key perennial crop susceptible to a diverse range of arthropod pests that account for their life with at least one soil inhabitant stage. In this study, we investigated, for the first time, the occurrence of EPNs and associated soil organisms in olive groves managed with different practices. We surveyed 89 commercial olive groves located in Andalusia (Southern Spain) and differently handled for pest management (conventional vs. organic), soil management (tilling vs. cover cropping), and irrigation regime (rain feed vs. drip-irrigation). By using species-specific primers-probe sets and quantitative real-time PCR approaches, we screened the occurrence of nine species of EPNs, five free-living nematodes (FLNs), and six nematophagous fungi (NF). We found EPNs in 23.6% of the sites, identifying only two EPN species: Steinernema feltiae (15.7%) and Heterorhabditis bacteriophora (7.9%). Pest and soil management did not affect EPN abundance, but drip irrigation increased their occurrence (P < 0.025). On the contrary, we recorded lower FLN numbers in irrigated groves (P = 0.003), particularly for Oscheius tipulae and Pristionchus maupasi. Regarding NF, both organic management (P < 0.001) and drip irrigation (P < 0.035) enhanced their abundance. Four abiotic explanatory variables (extractable P, clay content, elevation, and precipitation) explained 85.6% of the EPN, FLN, and NF species variation in multivariate analysis. Overall, drip irrigation in the olive groves enhanced the EPN community but also NF growth, natural enemies of nematodes. Additional studies are required to determine the best combination of alternative strategies that will enhance a balanced soil biota in olive groves in Mediterranean regions and other areas where this crops is cultivated that enable conservation ecosystem services, such as those provided by the EPNs.