The extraction of nanoparticles (NPs) from complex matrices and subsequent storage can potentially alter the NPs physicochemical properties and hinder cross-study comparisons. Most NP extraction methods are designed and tested at high nanoparticle concentrations, although (eco)toxicological and regulatory monitoring programs require methods capable of analyzing NPs at environmentally relevant concentrations (lower ppb range). In this study, we investigated how extraction methods affect the characteristics of PVP coated and citrate-stabilized silver NPs (AgNPs) spiked into soil, sewage sludge, and biological samples at environmentally relevant concentrations using Single Particle Inductively Coupled Plasma Mass Spectrometry spICP-MS). Further we investigated the impact of storage temperature (-80°C to 21°C) and storage duration (1-28 days) on the particle characteristics such as particle size.We found that aqueous AgNPs samples with low ionic strength media retained their original characteristics (like particle size, particle concentration and particle-based Ag mass) when preserved at 4°C for up to 28 days. AgNPs dispersed in high ionic strength media were however better preserved at -80°C. Among the extraction agents, tetrasodium pyrophosphate was more efficient in extracting AgNPs from soil and sewage sludge matrices, while Proteinase K was more suitable for biological samples from organisms (earthworms or fish).Although our study focused only on AgNPs, it provides crucial information to aid interlaboratory comparisons and data interpretation for (eco)toxicological studies.