The mechanisms of defect formation in single crystalline epitaxial iron garnet thin films implanted with intermediate energy He+, B+, and Si+ ions have been investigated. X‐ray diffraction and modeling of the implantation process are used to show the effectiveness of defect formation from the electronic energy losses of ion implants decelerating in the target. High temperature diffractometry demonstrates the existence of two centers of disorder in the crystal lattices of ion‐implanted thin films: one due to the defect formation from the electronic energy losses and the other – from the nuclear energy losses of the implant ions.