In life science and health research one observes a continuous need for new concepts and methods to detect and quantify the presence and concentration of certain biomolecules—preferably even in vivo or aqueous solutions. One prominent example, among many others, is the blood glucose level, which is highly important in the treatment of, e.g., diabetes mellitus. Detecting and, in particular, quantifying the amount of such molecular species in a complex sensing environment, such as human body fluids, constitutes a significant challenge. Surface-enhanced infrared absorption (SEIRA) spectroscopy has proven to be uniquely able to differentiate even very similar molecular species in very small concentrations. We are thus employing SEIRA to gather the vibrational response of aqueous glucose and fructose solutions in the mid-infrared spectral range with varying concentration levels down to 10 g/l. In contrast to previous work, we further demonstrate that it is possible to not only extract the presence of the analyte molecules but to determine the quantitative concentrations in a reliable and automated way. For this, a baseline correction method is applied to pre-process the measurement data in order to extract the characteristic vibrational information. Afterwards, a set of basis functions is fitted to capture the characteristic features of the two examined monosaccharides and a potential contribution of the solvent itself. The reconstruction of the actual concentration levels is then performed by superposition of the different basis functions to approximate the measured data. This software-based enhancement of the employed optical sensors leads to an accurate quantitative estimate of glucose and fructose concentrations in aqueous solutions.