The temperature and concentration dependent phase diagrams of zero-valent copper, cobalt, and iron intercalated bismuth selenide are investigated using in situ transmission electron microscopy. Polytypic phase transitions associated with superlattice formation along with order-disorder transitions of the guest intercalant are determined. Dual-element intercalants of CuCo, CuFe, and CoFe-Bi2Se3 are also investigated. Hexagonal and striped domain formation consistent with two-dimensional ordering of the intercalant and Pokrovksy-Talapov theory is identified as a function of concentration. These studies provide a complete picture of the structural behavior of zero-valent metal intercalated Bi2Se3.