In January 2023, the derogation loophole was closed on “emergency authorisations” for the use of three out of five neonicotinoids in all EU states. In this study, we analysed the sorption/desorption behaviour and kinetic parameters of acetamiprid and thiacloprid, the two neonicotinoids that are still approved for use, either regularly or under emergency authorisations in the EU, and widely used worldwide. Sorption and desorption curves in four soils with different organic matter content were analysed using four kinetic models, namely, Lagergren’s pseudo first-order model, two-site model (TSM), Weber–Morris intraparticle diffusion model and Elovich’s model. Kinetic parameters were correlated to soil physico-chemical characteristics. To determine the mutual influence of soil characteristics and sorption/desorption parameters in the analysed soils, a factor analysis based on principal component analysis (PCA) was performed. Even though the two insecticides are very similar in size and chemical structure, the results showed different sorption/desorption kinetics. The model that best fits the experimental data was TSM. Thiacloprid showed a more rapid sorption compared to acetamiprid, and, in all soils, a higher proportion sorbed at equilibrium. Intra-particle diffusion seemed to be a relevant process in acetamiprid sorption, but not for thiacloprid. Desorption results showed that acetamiprid is more easily and more thoroughly desorbed than thiacloprid, in all soils. The kinetic behaviour differences stem from variations in molecular structure, causing disparate water solubility, lipophilicity, and acid–base properties.