Analyte delocalisation is a significant challenge in matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI). In this study, we present a novel approach to decrease this phenomenon and improve analyte detection by modifying the wettability of indium tin oxide (ITO) coated glass slides, commonly used for tissue analysis, using plasma polymer coatings. These coatings are stable under vacuum conditions and during the ionization process. Surface coatings had minimal impact on the signal-to-noise ratio of peptides, proteins, and lipids in profiling experiments, where analytes were directly spotted on the surface, but it had a pronounced effect in MALDI MSI. When analysing fresh frozen murine brain sections, specifically the highly hydrophobic surface coating increased the signal-to-noise ratio for over 280 putative phospholipids by 2 to 40-fold compared to uncoated ITO slides. Notably, previously analytes of interest in brain research such as cholesterol were easily detected. This is the first application of plasma polymers to modify ITO slides for MALDI MSI, resulting in a significant enhancement of lipid ion intensity.