A complete characterization of yacon syrup was performed by analytical techniques, including NMR and UPLC-QTOF-MSE. The effect of the different stages of yacon syrup production on fructooligosaccharides (FOS) and chlorogenic acid (CGA) contents were also evaluated. As a result, in addition to higher levels of FOS and CGA, some mineral elements, such as K, Ca and P, and essential amino acids, such as tryptophan, valine, and threonine, were determined in yacon syrup. Twenty-five compounds were putatively identified, and the main compounds were phenolics derived from quinic and trans-cinnamic acids. Considering the different stages of yacon syrup production, the results indicate that the contents of FOS and CGA were maintained in the pulping, enzymatic maceration and microfiltration, leading to a concentration of these components in the last stage of processing (vacuum concentration). These results will be used to fortify this innovative and promising product in the area of functional foods.