NMR is a well‐established analytical technique that enables the identification and quantification of several compounds in complex mixtures. The implementation of automated analysis software enhances this process by comparing sample spectra with a library of standard reference spectra. One of the key parameters in libraries is the signal line width; however, this may result in a concentration bias for compounds with broad signals, particularly those that are complexing. This study aims to evaluate the quantification of seven compounds commonly present in wine with complexing activity. Four automatic programs and manual deconvolution were used to quantify mixtures of these compounds at known concentrations, both in the presence of cations and with the addition of ethylenediamine‐tetraacetate (EDTA) as a chelating agent. Additionally, malate was quantified in a wine sample using the standard addition method, both with and without EDTA. The findings illustrate that three of the programs, which employ the signal width value, underestimate compound concentrations in the presence of cations due to signal broadening. This error was mitigated by the EDTA addition. In contrast, the remaining software, which did not utilize signal line width, obtained similar concentrations in both cases. Future investigations involving the automatic analysis of compounds with complexing activity should take care of sample preparation and/or algorithm selection. Furthermore, future software development should consider allowing flexible adjustments of signal line width in their workflow.