Cellular membrane lateral organization, in particular the assembly of lipids in domains, is difficult to evaluate at high resolution. Here, we used atomic force microscopy (AFM) to investigate at high-resolution lipid membranes containing variable amounts of sphingomyelin (SM) and cholesterol (Chol), two abundant membrane lipids. To this end, we developed new AFM tip functionalization strategies to specifically probe SM and Chol. Multiparametric AFM imaging allowed us to highlight the lateral submicrometric organization of these two lipids within lipid bilayers through the simultaneous topographic evidence of different phase regimes together with the extraction of their nanomechanical properties and the specific detection of lipid moieties by functionalized AFM probes. The combination of AFM topography and nanomechanical mapping with specific probes for molecular recognition of lipids represents a novel approach to identify lipid-enriched domains in supported bilayers and offers a unique perspective to directly observe lipid assemblies in living cells.