Formation damage has a negative impact on the productivity of a well. Hence, its mechanism needs to be well understood to be able to mitigate it. Secondary damage is a form of formation damage that occurs during the removal process of barite filter cake layer but has received less attention. This study focuses on examining the secondary damage that occurs during the removal process of barite filter cake layer using chelating agents. Ethylenediaminetetraacetic acid (EDTA) with a concentration of 20% was employed as an effective treatment solution for removing the barite filter cake. EDTA was prepared as a pure solution (referred to as EDTA-K) and saturated with barium (referred to as EDTA-Ba) to simulate the solution state after the completion of filter cake removal. Experiments were conducted using different rock samples, including a sandstone and a carbonate core, to investigate the interaction between the chelating agent and the formation through a core flooding system. Nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI) were applied to evaluate the alterations in the inner pore structure, and pore size distribution due to the EDTA reactivity. Furthermore, the changes in rock samples’ permeability were examined. Results showed that the reactivity of EDTA varies depending on the rock type and the presence of specific ions. EDTA exhibited limited reactivity with sandstone samples because of its weak ability to react with the silicate matrix and limited content of clay minerals containing Al3+ and Mg2+, highlighting a lower potential for secondary formation. In contrast, carbonate samples demonstrated higher reactivity with EDTA, leading to enhanced permeability. However, the precipitation of barium within the pores of carbonate rocks was observed, which can be considered as a significant level of secondary formation damage. Ab initio calculations supported the experimental findings by demonstrating the binding ability of EDTA with different ions.