Extractions methods based on ultrapure water, tetramethylammonium hydroxide (TMAH), and tetrasodium pyrophosphate (TSPP) were applied to faeces collected from two in vivo experiments of pigs and chickens fed with a silver-based nanomaterial to study the fate and speciation of silver. For TMAH extraction, cysteine and CaCl2were used to evaluate their stabilization effect on the silver forms. The analytical techniques single-particle inductively coupled plasma mass spectrometry (SP-ICP-MS), hydrodynamic chromatography hyphenated to ICP-MS (HDC-ICP-MS) and asymmetric flow field flow fractionation coupled to ICP-MS (AF4-ICP-MS) were applied to the simultaneous detection of particulate and dissolved silver. Results have shown that water extraction was a suitable option to assess the environmental release of silver, with percentages of 3 and 9% for faeces of pigs and chickens, respectively. The use of TMAH extraction combined with SP-ICP-MS analysis was useful to characterize Ag-containing particles (less than 1%). Both stabilizers, cysteine and CaCl2, have a similar effect on silver nanoparticle preservation for chicken faeces, whereas cysteine-Triton was better for pig samples. In any case, silver extraction efficiency with TMAH was low (39–42%) for both types of faeces due to a matrix effect. TSPP followed by ICP-MS enabled the fractionation of the silver in the faeces, with silver sulphide (41%) and ionic silver (62%) being the most abundant fractions.Graphical AbstractSupplementary InformationThe online version contains supplementary material available at 10.1007/s00604-023-05777-0.