The search for carbonaceous matter in Martian rocks is the key to evaluating their potential biosignatures. Studying carbonaceous matter preserved within Earth’s basaltic analogs provides critical insights into the mineral–organic interactions that may also occur on Mars. To characterize molecular-level chemical information of carbonaceous matter, correlative surface-sensitive approaches such as Focused Ion Beam Scanning Electron Microscopy (FIB-SEM), Secondary Ion Mass Spectrometry (SIMS), and Atomic Force Microscopy Infrared Spectroscopy (AFM-IR) are employed. In this study, we developed a correlative microanalytical protocol starting with the ex-situ FIB-SEM lift-out, in which lamellae from a Mars-analog basalt were transferred onto a clean silicon substrate using a glass-needle nanomanipulator. The lamellae were then analyzed sequentially by Time-of-Flight SIMS (TOF-SIMS), AFM-IR, and Nano-scale Secondary Ion Mass Spectrometry (NanoSIMS). Specifically, spatially and chemically co-registered TOF-SIMS, AFM-IR, and NanoSIMS analyses provided complementary insights into the same region, correlating organic distribution, molecular vibrations, and isotopic compositions within mineral matrices. Together, these results demonstrate that the established correlative microanalytical protocol in this study effectively integrates sample preparation and multi-modal surface analyses, providing a framework for investigating planetary materials and future Mars samples.