The encapsulation of carbon nanotubes (CNTs) to form a reconfigurable conglomerate within iron oxide microcapsules is demonstrated. The individual CNTs conglomerate and form a core inside the capsule upon exposure to high temperature, while they scatter when subjected to mild sonication at low pH. The assembly/disassembly of CNTs within the capsule was reversible and could be repeated by alternate heating and sonication. Also, the fabrication protocol could be used for the generation of various multifunctional hollow structures. To test the feasibility of using the capsules in real applications the capacity of the capsules as a heavy metal ion remove explored. The resulting capsules: showed an excellent ability to remove lead and chromium ions. In addition, desorption of the metal ions adsorbed on the CNTs could be induced by exposure to low pH. Thus, encapsulated CNTs might be a recyclable, environmentally friendly agent for the removal of heavy metal ions.