Capacity fading of lithium-ion batteries with Mn-containing cathodes is closely related to Mn dissolution from the cathode and, more importantly, the subsequent Mn deposition on the anode. In this work, we propose a new method for solving the Mn deposition issue: tuning the Mn deposition instead of simply decreasing the concentration of Mn deposited on the anode. Two commonly used electrolyte additives, fluorinated ethylene carbonate and vinylene carbonate, are found to improve the cycle performance of the battery but, surprisingly, to enhance the Mn deposited on the anode at the same time. According to the ion-exchange model in our previous work, this increased Mn²⁺ deposition can be attributed to the increased amount of the Li⁺ ions in the additive-modified solid-electrolyte interface (SEI), as the Mn deposition can occur via an ion-exchange reaction between the Li⁺ in the SEI and the Mn²⁺ in the electrolyte. The improved capacity retention can be attributed to the enhanced robustness of the SEI layers against the attack of Mn²⁺ ion because of the sufficient amount of mobile Li⁺ in the SEI layer for ion transport. This work sheds new light on solving the capacity fade issue of Mn-based Li-ion batteries by manipulating the Mn-Li ion-exchange process.