Silver nanoparticles (AgNPs) are widely used in all branches of industry. However, their mechanisms of action towards moulds have not been studied yet. Thus we conducted this study in which we have used laser desorption/ionization time-of-flight mass spectrometry (LDI-ToF-MS) analysis to determine metabolomic changes, and microscopic analysis (transmission electron microscopy, fluorescent microscopy) to observe changes in mould cells. The AgNP treatment caused the downregulation of 162 (15 ppm) and 284 (62 ppm), and 19 (15 ppm) and 29 (62 ppm) metabolites of Aspergillus niger and Penicillium chrysogenum, respectively. All influenced features were below m/z 600 (mass-to-charge ratio). We have observed silver ions and their clusters (Ag, Ag2, and Ag3) accumulated in the mould mycelium. As well as, mono-silver ion adducts with nucleotide derivatives (Coenzyme A), amino acids (phenylglycine), peptides (LeuSerAlaLeuGlu) and lipids (fatty acids, diacylglycerophosphoglycerols, monoglicerides and glycerophospholipids). The ultrastructure analysis revealed many sever alterations due to the action of AgNPs, such us shortening and condensation of hyphae, ultrastructural reorganisation, cell plasmolysis, increased vacuolisation, numerous membranous structures, collapsed cytoplasm, accumulation of lipid material, condensed mitochondria, disintegration of organelles, nuclear deformation, condensation and fragmentation of chromatin, creation of apoptotic bodies, as well as a new inside cell wall in P. chrysogenum.