Natural products continue to be major sources of bioactive compounds and drug candidates not only because of their unique chemical structures but also because of their overall favorable metabolism and pharmacokinetic properties. The number of publicly accessible natural product databases has increased significantly in the past few years. However, the systematic ADME/Tox profile has been reported on a limited basis. For instance, BIOFACQUIM was recently published as a public database of natural products from Mexico, a country with a rich source of biomolecules. However, its ADME/Tox profile has not been reported. Herein, we discuss the results of an in-depth ADME/Tox profile of natural products in BIOFACQUIM and other large public collections of natural products. It was concluded that the absorption and distribution profiles of compounds in BIOFACQUIM are similar to those of approved drugs, while the metabolism profile is comparable to that in the other natural product databases. The excretion profile of compounds in BIOFACQUIM is different from that of the approved drugs, but their predicted toxicity profile is comparable. This work further contributes to the deeper characterization of natural product collections as major sources of bioactive compounds with therapeutic potential.