Because of their high tunability and surface area, metal-organic frameworks (MOFs) show great promise as supports for metal nanoparticles. Depending on the synthesis route, MOFs may contain defects. Here, we show that highly crystalline MIL-100(Fe) and disordered Basolite® F300, with identical iron 1,3,5-benzenetricarboxylate composition, exhibit very divergent properties when used as a support for Pd nanoparticle deposition. While MIL-100(Fe) shows a regular MTN-zeotype crystal structure with two types of cages, Basolite® F300 lacks long-range order beyond 8Å and has a single-pore system. The medium-range configurational linker-node disorder in Basolite® F300 results in a reduced number of Lewis acid sites, yielding more hydrophobic surface properties compared to hydrophilic MIL-100(Fe). The hydrophilic/hydrophobic nature of MIL-100(Fe) and Basolite® F300 impacts the amount of Pd and particle size distribution of Pd nanoparticles deposited during colloidal synthesis and dry impregnation methods, respectively. It is suggested that polar (apolar) solvents/precursors attractively interact with hydrophilic (hydrophobic) MOF surfaces, allowing tools at hand to increase the level of control over, for example, the nanoparticle size distribution.