Poly(3-hexylthiophene) (P3HT) adsorption on the quasihexagonally reconstructed Au(001) surface via differentially pumped electrospray deposition is reported. In situ scanning tunneling microscopy reveals a complex adsorption behaviour of P3HT. Weakly adsorbed chains are found which exhibit a 2D random coil like chain configuration across the reconstructed surface. Other molecules are constraint into a fully stretched configuration along the [110] high-symmetry directions of the square Au(001) lattice indicating a strong molecule-substrate interaction. This adsorption is accompanied by local lifting of the reconstruction underneath the polymer chains.