Mineral fertilizers are indispensable for the intensification of plant production in agriculture. This process can cause a significant odour nuisance for the environment due to organic compounds content in apatites and phosphorites converted into fertilizers. The following chemical compounds are emitted to the gas phase among others: hydrogen sulphide, organic sulphides and (methyl, ethyl, isopropyl, butyl) disulphides, chain hydrocarbons, organic oils, waxes and carboxylic acids. A method using gas chromatography analysis with the mass detector (TD-GS-MS), to determine trace concentrations, was developed and tested for the assessment of odour nuisant substances emission from these processes. Application of additional thermal desorber to enable the intense desorption of the investigated organic compounds (previously adsorbed on classical sorbents) in the industrial research has been taken into consideration. In effect it facilitates the accumulating substances to be analyzed at short time interval providing identifying measurements. The technique has been verified during the investigation of the substances emitted in fertilizers processes at Maroko phosphorite decomposition. The organic sulfur compounds, aliphatic and aromatic hydrocarbons have been detected.