A new calibration method based on the use of headspace solid-phase microextraction (HS-SPME) and in-fiber internal standardization, combined with gas chromatography coupled to mass spectrometry (GC/MS) was developed for quantifying Se volatile organic species released by plants exposed to chitosan-modified selenium nanoparticles (Cs-SeNPs). The effect of several parameters affecting extraction and separation of the selected organic species of selenium (dimethylselenium (DMSe), diethylselenium (DESe) and dimethyldiselenium (DMDSe)) and deuterated dimethyl sulphide (d⁶-DMS) employed as internal standard were studied and optimized using an experimental design. The developed methodology was applied for quantifying the volatile selenium compounds produced over time by the plant species Raphanus sativus and Brassica juncea grown in hydroponic solution containing 5 mg Se L⁻¹ in the form Cs-SeNPs. The procedure employed consisted in two steps. Volatile selenium species released from the plants were first extracted in the SPME fiber located at the headspace of a box with a fixed volume. Subsequently, the internal standard placed in a vial subjected to the same conditions as plants was extracted on the same fiber than the one previously used for extracting selenium compounds. Finally the extracted compounds were separated and analyzed by GC/MS. Results evidenced Cs-SeNPs biotransformation into DMSe and DMDSe by both plants species during growing stage, in amounts of the order of ng. Additionally, the resulting data were submitted to multifactorial ANOVA to evaluate the influence of plant type and time of exposure to Cs-SeNPs on the production of volatile selenium compounds.