This work describes mass recovery processes of flooded archival materials at industrial scale. The presence of fungi on paper represents a threat to the integrity of the document because they degrade cellulose, one of the main components of paper. Gamma radiation treatments are investigated as mass disinfection agents for their high penetrating power, speed of treatment, and absence of risk due to chemical residuals. We compared two different recovery processes: thermal drying followed by gamma irradiation and gamma irradiation followed by thermal drying. Both these processes were conducted simultaneously on naturally contaminated archival items and on paper specimens artificially contaminated with species test. Efficacy was assessed by culture method and ATP assay, right after the treatments and after four years of storage at room temperature. Coupling gamma irradiation with a drying step with dry heat at 55–60 °C reduces the fungal loads on natural items up to levels close to the detection limits, and the reduction is maintained after four years. On artificial specimens, spore germination is completely inhibited, mycelia growth is also highly affected, but the melanised test species appear to be more resistant. A synergistic effect between gamma irradiation, water content, and thermal drying is highlighted in this paper.