We report on the impact of partial fluorination of para-sexiphenyl (6P) on the growth mode when deposited on the non-polar ZnO(101̄0) surface. The evolution of the thin film structure and morphology is monitored by in situ atomic force microscopy and in situ real-time X-ray scattering. Both 6P and its symmetrical, terminally fluorinated derivative (6P-F4) grow in a highly crystalline mode, however, with a distinctly different morphology. While 6P films are characterised by the formation of two different phases with three-dimensional nanocrystallites and consequently a rather rough surface morphology, layer-by-layer growth and phase purity in case of 6P-F4 prevails leading to smooth terraced thin films. We relate the different growth behaviour to specifics of the thin film structure.