Fused silica and hydride-based particles were characterised. Atomic distributions on each particle surface were determined using energy-dispersive X-ray spectroscopy. Increased surface carbon content, with decreasing oxygen and silicon, correlated well with more negative zeta potential values (R² being 0.92, 0.95 and 0.86 respectively). Extraction performance of hydride particles for resveratrol and flavonoid standards, as well as analytes extracted from dark chocolate using dispersed particles was then performed, analysed by gas chromatography-quadrupole mass spectrometry analysis after derivatisation. The extraction performance of fused silica, hydride and diamond hydride was apparently governed by their zeta potentials. However, ligand-analyte interactions were dominant in extraction using particles modified with larger ligands, predicted using Abraham descriptors. Separations conducted in pipette tips packed with 40 mg of phenyl, BDC18 and cholesteryl modified particles were illustrated. The established analytical methods are expected to be useful for a small-scale characterisation of silica-based materials as well as broadening the concept of stationary/mobile phase interface.