This paper presents a comprehensive study on the enhancements made to the heavy-ion microbeam (H-MB) and light-ion microbeam (L-MB) systems at the Takasaki Institute for Advanced Quantum Science, part of the National Institutes for Quantum Science and Technology (QST), and their implications for future research in ion microbeam technology. Our work addresses the critical need for submicron beam sizes in advanced ion microbeam applications, a challenge previously unmet due to limitations in the original system designs and aging components. The manuscript details the extensive upgrades undertaken for both the H-MB and L-MB systems, including the implementation of new quadruple magnets, refined demagnification strategies, and advanced control systems, culminating in the successful formation of submicron ion beams. The meticulous alignment procedures for both the H-MB and L-MB have enabled precise ion beam focusing. The current beam sizes have been measured at 1.0 × 1.1 µm2 with a beam current of approximately 10 pA for the H-MB, and 500 × 600 nm2 with a beam current of approximately 50 pA for the L-MB at a 3 MeV H+ beam.