Abstract: Two-dimensional (2D) kagome lattice metals are interesting because they display flat electronic bands, Dirac points, Van Hove singularity, and can have interplay amongst charge density wave (CDW), magnetic order, and superconductivity. In kagome lattice antiferromagnet FeGe, a short-range CDW order was found deep within an antiferromagnetically ordered state interacting with magnetic order [1]. Surprisingly, the post-growth annealing process of FeGe at 560◦C can suppress the CDW order while annealing at 320◦C induces a long-range CDW order, with the ability to cycle between the states repeatedly by annealing [2]. Here we use transport, neutron scattering, scanning transmission electron microscopy (STEM), and muon spin rotation (μSR) experiments to unveil the microscopic origin of the annealing process and its impact on magneto-transport, CDW, and magnetic properties of FeGe. We find that 560◦C annealing creates germanium vacancies uniformly distributed throughout the FeGe kagome lattice that prevent the formation of Ge-Ge dimers necessary for the CDW order. Upon annealing at 320◦C, the system segregates into stoichiometric FeGe regions with long-range CDW order and regions with stacking faults that act as nucleation sites for the CDW. The presence or absence of CDW order greatly affects the anomalous Hall effect, incommensurate magnetic order, and spin-lattice coupling in FeGe, thus placing FeGe as the only known kagome lattice material with a tunable CDW and magnetic order potentially useful for sensing and information transmission.