To make a drug work better, the active substance can be incorporated into a vehicle for optimal protection and control of the drug delivery time and space. For making the drug carrier, the porous metal−organic framework (MOF) can offer high drug-loading capacity and various designs for effective drug delivery performance, biocompatibility, and biodegradability. Nevertheless, its degradation process is complex and not easily predictable, and the toxicity concern related to the MOF degradation products remains a challenge for their clinical translation. Here, we describe an in-depth molecular and nanoscale degradation mechanism of aluminum-and iron-based nanoMIL-100 materials exposed to phosphate-buffered saline. Using a combination of analytical tools, including X-ray photoelectron spectroscopy, nuclear magnetic resonance spectroscopy, small-angle X-ray scattering, and electron microscopy, we demonstrate qualitatively and quantitatively the formation of a new coordination bond between metal(III) and phosphate, trimesate release, and correlation between these two processes. Moreover, the extent of material erosion, i.e., bulk or surface erosion, was examined from the transformation of nanoparticles' surface, morphology, and interaction with water. Similar analyses show the impact of drug loading and surface coating on nanoMIL-100 degradation and drug release as a function of the metal−ligand binding strength. Our results indicate how the chemistry of nanoMIL-100(Al) and nanoMIL-100(Fe) drug carriers affects their degradation behaviors in a simulated physiological medium. This difference in behavior between the two nanoMIL-100s enables us to better correlate the nanoscale and atomic-scale mechanisms of the observed phenomena, thus validating the presented multiscale approach.