In this work we combine scanning tunneling microscopy, near-edge X-ray absorption fine structure spectroscopy, X-ray photoemission spectroscopy and density functional theory to resolve a long-standing confusion regarding the adsorption behaviour of benzonitrile on Si(001) at room temperature. We find that a trough-bridging structure is sufficient to explain adsorption at low coverages. At higher coverages when steric hindrance prevents the phenyl ring lying flat on the surface, the 2+2 cycloaddition structure dominates.