The expansion of wheat crops (Triticum spp.) to the Brazilian Cerrado highlights the need to use pathogen-free seeds. This study aimed at evaluating the efficacy of nanoparticles (NPs) and photodynamic therapy (PhT) in inhibiting the in vitro growth of the fungus Alternaria alternata, in its treatment and control in naturally contaminated wheat seeds, and in the physiological quality of the seeds. The efficacy of NPs (ZnOCl, ZnOCl:1Cu, ZnOCl:0.1Ag; ZnO:1Cu, ZnO, and ZnO:1Ag) and PhT using methylene blue (MB) and toluidine blue (TB) dyes was evaluated in inhibiting the mycelial growth of A. alternata and in the treatment and control of the pathogen in wheat seeds by evaluating germination, emergence, GSI, ESI, accelerated ageing, and health. All NPs at 2.5 and 5 mg mL-1 concentrations and the dyes MB, TB, MB + TB at 50 and 100 µmol L-1 inhibited mycelial growth and reduced the incidence of A. alternata in the seeds. The NP ZnO:1Ag at 5 mg mL-1 and the MB + TB dye at 100 µmol L-1 were the most effective in inhibiting mycelial growth. NPs and PhT did not affect the physiological quality of seeds and controlled A. alternata in wheat seeds, demonstrating potential use in the treatment and control of the pathogen in wheat seeds.