Micropollutants such as pharmaceutical active compounds, present at high concentration in hospital wastewater (HWW), pose both environmental and human health challenges. Fungal reactors can effectively remove such contaminants and produce non-toxic effluents, but their ability to operate for a long period of time is yet to be demonstrated in real hospital wastewater. Several process variables need to be studied beforehand. Here, variables: pellet size, aeration and carbon-to-nitrogen ratio are studied in continuous operations with real HWW. Moreover, a novel strategy for inoculum production that could reduce economical and operational costs is proposed and tested. Optimum pellet size was found to be 2 mm and an aeration of 0.8 L min-1 was needed to maintain fungal viability. The carbon-to-nitrogen ratio of 7.5 was selected and the pellet production time was reduced from 6 to 3 days. The novel low-cost inoculum preparation produced pellets with the same characteristics as the traditionally prepared ones.