Black root rot complex and crown rot of strawberry caused by soilborne fungi limit sustainable strawberry production in the northeastern United States, especially in perennial systems, including matted row and plasticulture. As pathogen populations build up over time in the rhizosphere and infect the root system, feeder roots are pruned, which diminishes nutrient and water uptake and causes stunted plant growth or death. Alternative management options are needed for many organic and small growers who can't use chemical fumigants due to new regulations and potential health hazards. Strawberry plug plants were grown on beneficial microbe-inoculated or uninoculated planting mix followed by transplanting in fruiting field plots that either was biofumigated with mustard cover crop (MCC), anaerobically disinfested (ASD), or left untreated. Different combinations of plug plants and field plot treatments were used to determine the efficacy of individual treatments or synergistic effects from combination treatment. Plug plants were transplanted in pretreated plastic mulched raised beds and grown following a typical organically recommended production system. Plants grown on TerraGrow (TG)-inoculated planting mix showed enhanced plant vigor in the fruiting field compared with untreated plants. Weeds that grew through planting holes were significantly (P ≤ 0.045) suppressed in ASD plots compared with untreated plots in the first year. Plants treated with a combination treatment of TG and ASD had significantly higher fruit yield in both years (2019 and 2020), although the difference was greater in the second year. Plant vigor and survival in treated plots except MCC were also significantly higher in the second year compared with the untreated control. Suppression of pathogenic microbes and plant vigor improvement in treated plots appear to be the factors providing beneficial effects and higher net economic return. Taken together, our results suggest that a combination of beneficial microbes and ASD could be an alternative to synthetic fumigation in a perennial strawberry production system.