Byproducts in metalnanoparticle synthesis can interfere with nanomaterial formation and self-assembly, as well as the perceived nanomaterial properties. Such syntheses go through a complicated series of intermediates, making it difficult to predict byproduct chemistry and challenging to determine experimentally. By a combined experimental and theoretical approach, the formation of organic byproducts is mapped out for the synthesis of gold nanoparticles with Good’s buffer 2-(N-morpholino)ethanesulfonic acid. Comprehensive nuclear magnetic resonance studies supported by mass spectrometry, ultraviolet–visible spectroscopy, and density functional theory reveal a number of previously unidentified byproducts formed by oxidation, C–N bond cleavage,and C–C bond formation. A reaction mechanism involving up to four consecutive oxidations is proposed. Oligomeric products with electronic transitions in the visible range are suggested. This approach can be extended broadly and lead to a more informed synthesis designand material characterization.