Microfluidic diffusional sizing (MDS) is a powerful technique in bioanalytical research, offering a broad spectrum of applications based on its simple yet effective principle—relating diffusion speed to particle size. However, its reliance on selectively fluorescently labeled analytes poses challenges when studying lipid nanoparticles or complex biological samples, such as crude cell extracts. Fluorescent universal lipid labeling for MDS (FULL-MDS) is a sparse, noncovalent labeling method designed to overcome this limitation. Using widely available fluorophores such as Nile blue and Nile red, FULL-MDS enables robust hydrodynamic size determination of lipid nanoparticles in both simple synthetic and complex biological samples. Moreover, its labeling approach is straightforward, cost-effective, and compatible with other hydrodynamic sizing techniques, making it highly adaptable for diverse research applications. FULL-MDS therefore holds significant potential for advancing the characterization of lipid nanoparticles in both fundamental and applied sciences.