Simple Summary: Human activities such as heavy industry and transport have significantly increased the levels of many poisonous chemicals in the human environment. Among these chemicals are heavy metals, which pose a great risk to human health because they cannot decompose and cannot be eliminated from the human body by metabolic processes. Volcanic stone called clinoptilolite is inert and extremely porous, and can capture heavy metals into its meshed structure. Therefore, it can be used as a food supplement for detox purposes. Several clinical studies have already indicated its detoxifying, antioxidant and anti‐inflammatory effects. In our experiment, we fed healthy rats with clinoptilolite, which was milled to fine dust to improve performance, for three months. Two forms were used: tribomechanically activated zeolite and Panaceo‐Micro‐Activated zeolite. Upon completion of the administration period, we observed the impact of clinoptilolite dust on the metallic composition in different rat tissues and bloodstream. Our results showed that this activated natural stone had indeed released metallic toxicants from the rat organs to the bloodstream, which indicates a detoxification process. Abstract: Heavy metals are dangerous systemic toxicants that can induce multiple organ damage, primarily by inducing oxidative stress and mitochondrial damage. Clinoptilolite is a highly porous natural mineral with a magnificent capacity to eliminate metals from living organisms, mainly by ion‐exchange and adsorption, thus providing detoxifying, antioxidant and anti‐inflammatory medicinal effects. The in vivo efficiency and safety of the oral administration of clinoptilolite in its activated forms, tribomechanically activated zeolite (TMAZ) and Panaceo‐Micro‐Activated (PMA) zeolite, as well as the impact on the metallic biodistribution, was examined in healthy female rats. Concentration profiles of Al, As, Cd, Co, Pb, Ni and Sr were measured in rat blood, serum, femur, liver, kidney, small and large intestine, and brain using inductively coupled plasma mass spectrometry (ICP‐MS) after a 12‐week administration period. Our results point to a beneficial effect of clinoptilolite materials on the concentration profile of metals in female rats supplemented with the corresponding natural clinoptilolite materials, TMAZ and PMA zeolite. The observed decrease of measured toxicants in the kidney, femur, and small and large intestine after three months of oral intake occurred concomitantly with their most likely transient release into the bloodstream (serum) indicative of a detoxification process.