There is an increasing demand for analytical tools to measure the internal concentrations of xenobiotic pollutants in small organisms. Such tools are required to determine exposure in ecotoxicological studies yet avoid sophisticated clean-up and enrichment techniques or large-scale experimental design. Thus, this paper presents a modified QuEChERS method coupled to gas chromatography tandem mass spectrometry (GC–MS/MS) for small volume organic samples. Ten zebrafish ( Danio rerio ) embryos were exposed to a 46-compound mixture at 10 ng/mL. After 72 h of exposure, they were extracted in 200 μL glass inserts using 70 μL of both acetonitrile and water. Volumes of 50 μL of extract were injected into a GC–MS/MS with a multi-mode inlet. Internal concentrations of zebrafish embryos could be reproducibly quantified in the lower nanogram per millilitre range at detection limits of 1–25 ng/mL and with recoveries of 63–133%. Internal concentrations varied over the tested range of compounds between 5.88 ± 0.616 ng/mL for dicofol and 232 ± 18.6 ng/mL for diflufenican. Detectability and recovery were best for compounds with a log D greater than four. As internal concentrations did not seem to exclusively depend on log D, biochemical transport processes could play an important role in the uptake kinetics of early zebrafish life stages. Graphical Abstract This paper presents an extraction and quantification method for 46 volatile organic compounds in zebrafish embryos. After exposure, pools of ten embryos were extracted with 70 μL acetonitrile applying a micro-QuEChERS approach. Internal embryo concentrations were analytically determined and quantified by large volumen injection gas chromatography tandem mass spectrometry (GC-MS/MS).