We report on the modification of zinc oxide thin films deposited by atomic layer deposition (ALD-ZnO) with various phosphonic acid derivatives. Particularly, three molecules differing by their spacer and functionalizing groups were tested: 2-aminoethylphosphonic acid (2-AEPA), 4-aminobenzylphosphonic acid (4-ABzPA) and 4-fluorobenzylphosphonic acid (4-FBzPA). The resulting surfaces were investigated with surface sensitive characterization techniques such as X-ray photoelectron spectroscopy and attenuated total reflection IR spectroscopy. We find differences in the phosphonic acid film growth, mostly driven by the nature of the functionalizing group: the amine-based molecules tend to cover the surface with disordered layers or multilayers whereas the 4-FBzPA layer rather exhibits features of a monolayer. Finally, 2-AEPA and 4-FBzPA have been used as a mean to passivate the reactive interface between ALD-ZnO and a hybrid organic inorganic metal halide perovskite. Morphological and structural studies were carried out with scanning electron microscopy and X-ray diffraction and solar cells using these layers as electron transport layers were synthetized. With a highest power conversion efficiency of 4.1%, the direct application of these surface modifications into complete devices is shown not to be enough to achieve high-efficiency solar cells with ALD-ZnO.