Silica nanostructured materials are important in many fields, including catalysis, imaging, and drug delivery, mainly due to the versatility of surface functionalization that can bestow a huge variety of chemical and physical properties. With most applications requiring precise control over this surface modification, characterization of surface composition and reactivity have become of extreme importance. We present a novel approach to track silica surface modification and quantify functional group coverage using only solution NMR. We test the method using different types of silica nanoparticles and surface modifications, to show that after dissolving the silica matrix, the 1H NMR spectra can be resolved for every single component of the mixture. By using an internal standard, we are able to quantify the density of ligands and follow their sequential modification. Our work presents a fast, accurate, and straightforward method for surface characterization of silica nanostructures, using widely available NMR spectroscopy and small amounts of sample.