Byproducts in metal nanoparticle 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 are mapped out for the synthesis of gold nanoparticles with the Good's buffer MES. 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 2 electronic transitions in the visible range are suggested. This approach can be extended broadly, and lead to more informed synthesis design and materials characterization.