Metal organic frameworks (MOFs) are a class of three-dimensional porous architectures that can be chemically functionalized. The ability of atomic layer deposition (ALD) to incorporate metal atoms or functional groups into MOFs offers an interesting alternative to chemically modify MOFs for applications such as catalysis and gas separation, for which transport, adsorption, and the reaction of gases are critical. Optimization of these deposition processes requires an understanding of the underlying reaction mechanisms that is best derived from in situ characterization. We have therefore combined in situ infrared spectroscopy, X-ray photoelectron spectroscopy with in situ sputtering, and ab initio calculations to elucidate the reaction mechanisms of the common ALD precursors trimethylaluminium (TMA), diethylzinc (DEZ), and TiCl4 with several Zr-MOFs containing hydroxyl (OH) and water (H2O) groups. Focusing on the OH and H2O groups is particularly revealing because it makes it possible to explore the reactivity dependence on the chemical and structural (i.e., sterics) environments. We find that the reactivity of the OH groups in the Zr6(μ3–OH)4(μ3–O)4(OH)x(OH2)y cluster node is highly dependent on their location, accessibility, and chemical environment. For instance, the activation temperature for the reaction of the OH groups of Zr6 clusters with TMA decreases with the node connectivity: 200, 150, and 24 °C for UiO-66-NH2, Zr-abtc, and MOF-808, respectively. Interestingly, the hydroxyl groups in unfunctionalized UiO-66 do not react with TMA molecules. Ab initio calculations reveal that the NH2 group is directly responsible for catalyzing this reaction by anchoring the TMA molecule in close proximity to the target OH group. Finally, we show that TMA easily reacts with water adsorbed on the external surfaces of wet MOF crystals at room temperature, forming a thick Al2O3 blocking layer on the periphery of the MOF crystals. These findings provide a basis for the design and modification of MOFs by ALD processes.