Nanoparticles of biocompatible iron carboxylate metal−organic frameworks (MOFs) or nanoMOFs are of great interest for biomedicine, in particular, for controlled drug release. However, little is known about the impact of their synthesis protocols on their defect content and the possible consequences in terms of physicochemical features and cytotoxicity. Here, we report for the first time how the defect content of the benchmark mesoporous iron trimesate MIL-100(Fe) (MIL stands for Materials of Institut Lavoisier) nanoparticles, with similar sizes but obtained from three different green synthesis routes, has a significant impact not only on their intrinsic porosity, stability in body fluids, drug loading capacity, and release but also shows a critical difference of in vitro toxicity and inflammatory response depending on the type of cell lines.