The effect of electrochemical pre-treatment on fungal treatment of pistachio processing wastewater (PPW) was investigated. Electrocoagulation (EC) and electrooxidation (EO) were used as electrochemical pre-treatment step before fungal treatment of PPW. Aluminum (Al/Al), iron (Fe/Fe), and stainless steel (SS/SS) electrode pairs were selected as anode/cathode for EC whereas boron doped diamond (BDD/SS) was preferred as anode/cathode electrode pairs for EO experiments in this study. The impact of current density (50–300 A/m²) and operating time (0–240 min) were tested for chemical oxygen demand (COD) and total phenol removal. After pre-treatment of PPW, four different fungus species (Coriolus versicolor, Funalia trogii, Aspergillus carbonarius, and Penicillium glabrum) were tested for further treatment. Penicillium glabrum supplied maximum COD and total phenol removal efficiency compared to other fungus strains. The combined electrochemical-assisted fungal treatment process supplied 90.1% COD and 88.7% total phenol removal efficiency when supported with EO pre-treatment. Pre-treatment of PPW with EO method provided better results than EC method for fungal treatment. Operating cost of the combined process was calculated as 6.12 US$/m³. The results indicated that the proposed combined process supplied higher pollutant removal compared to the individual electrocoagulation, electrooxidation, and fungal treatment process.