Scarcity of coyoteite hinders attempts to determine its atomic structure. It is unknown whether the oxygen and the hydrogen are present in the mineral as H2O molecules or OH− anions. However, because of the softness and the lamellar cleavage in the mineral, coyoteite structure might be close to that of valleriite, . Valleriite is a layered mineral, it consists of layers of (Mg0.68Al0.32(OH)2) and layers of (Fe0.07Cu0.93S2).
