The complex molecular assemblages were analysed in the soil gas phase after applying pine forest wastes (PFW) or sugarbeet vinasses (SBV) for soil-borne crop pests management. For this purpose, solid-phase micro-extraction (SPME) and gas chromatography (GC) were used coupled with mass spectrometry (MS). The organic wastes were applied either to Calcic Entisol or Haplic Arenosol moistened at field capacity and soil was covered with polyethylene sheet for 28−30 days to retain the volatiles. The PFW-treated soil mainly released volatile terpene hydrocarbons (trans-caryophyllene, β-myrcene and p-cymene), with α-humulene and ethylbenzotriazole prevailing in the untreated soil. After SBV application mainly alkyl compounds and alkylbenzenes were released, whereas cyclohexanone, limonene, butanone, acetic acid, camphor and benzaldehyde occurred in the untreated soil. Compound assemblages also depended on the increasing water saturation in terms of soil depth, with sulphur compounds prevailing in deep horizons. Our results showed that SPME can be directly applied to soils to provide valuable information on volatile products from organic amendments.