By use of spectroscopic sum frequency generation, we studied the molecular orientation in alkanethiolate self-assembled monolayers (SAMs) on Au(111) in situ during copper electrodepositon. The study is combined with an in situ scanning tunneling microscopy investigation under similar experimental conditions providing complementary real-space information. For the shortest molecule, hexanethiol (C6), an increase of the methyl group tilt angle during copper deposition from 22degrees to 83degrees is observed. Control experiments exclude a purely potential-induced origin indicating that Cu adsorption triggers the reorientation. The result is compatible with a rotation of the alkyl chain around its long axis accompanied by a change of surface-S-C angle. The structural change is partially reversible by copper stripping. The study demonstrates that slow metal deposition in the submonolayer range can have a major impact on the adsorbate structure of short chain thiolates.