An ‘Advanced Production System’ (APS) dramatically changed soil properties such as pH (P<0.001; panel A) compared to properties in conventional citriculture (CC). Responses by soil organisms to these changes included higher infestation rates by the bacterium Paenibacillus sp. on the entomopathogenic nematode Steinernema diaprepesi (P=0.05; panel B), which may have contributed to reduced numbers of infective juveniles (IJs) of native nematodes in APS plots (P=0.01; panel C). Display omitted •‘Advanced’ system (ACP) modifies soil properties and citrus trees mature earlier.•Native entomopathogenic nematode (EPN) numbers were reduced by ACP.•Higher Paenibacillus sp. infestation rate on S. diaprepesi in APS.•Nematophagous fungal responses to EPNs depended on EPN species.•APS has the potential to exacerbate herbivory by subterranean pests. Since its first detection in 2005, the bacterial disease huanglongbing (HLB or citrus greening) has emerged as a critical threat to the citrus industry in Florida. An “Advanced Production System” (APS) could mitigate the impact of HLB by bringing citrus trees into production more quickly and economically than conventional citriculture methods. However, unlike conventional practices, APS fertigates plants daily, thereby changing the soil properties in ways that might impact soil biota. We tested the hypothesis that changes to soil properties caused by APS would affect the abundance of native entomopathogenic nematodes (EPNs) and/or the survival of augmented EPNs. The densities of organisms at different trophic levels were measured by real-time qPCR in three experiments conducted in an ongoing field experiment. Target organisms included 6 entompathogenic nematodes, 5 nematophagous fungi (NF) and a phoretic bacterium, Paenibacillus sp. Soil properties, free-living nematodes and citrus fibrous roots were also measured. Compared to soil under conventional citriculture (CC), APS increased soil pH and Mg content, while reducing the electrical conductivity, and content of K, Mn and Fe. The naturally occurring EPN Steinernema diaprepesi was 5times less abundant in APS plots where these nematodes were more heavily encumbered by the phoretic bacterium Paenibacillus sp., which limits the foraging success of EPNs. In general, when EPNs were augmented in either treatment, fewer Steinernema riobrave than Heterorhabditis indica were recovered and recovery of both species declined rapidly over time. As seen with native S. diaprepesi, fewer augmented S. riobrave were recovered from APS plots in two of the three experiments, whereas the management system did not affect the recovery of H. indica. More of some endoparasitic and trapping NF were recovered from soil augmented with S. riobrave than with H. indica. However, variation in the responses of NF to the management systems suggests that these NF species were not primarily responsible for the steinernematid responses to APS. Although APS has the potential to reduce EPN populations and exacerbate herbivory by subterranean pests such as the root weevil Diaprepes abbreviatus, additional study of the physical causes of this effect may reveal ways to avoid the problem.