The study of dissolved organic matter (DOM) presents a significant challenge for environmental analyses and the monitoring of wastewater treatment plants (WWTPs). This is particularly true for the tracking of recalcitrant to biodegradation dissolved organic matter (rDOM) compounds, which is generated during the thermal pretreatment of sludge. This study aims to develop analytical and chemometric methods to differentiate melanoidins from humic acids (HAs), two components of rDOM that require monitoring at various stages of wastewater treatment processes due to their distinct biological effects. The developed method implements the separation of macromolecules through ultra-high-performance liquid chromatography size-exclusion chromatography (U-HPLC SEC) followed by online UV and fluorescence detection. UV detection was performed at 210, 254, and 280 nm, and fluorescence detection at six excitation/emission pairs: 230/355 nm, 270/355 nm, 240/440 nm, 270/500 nm, 330/425 nm, and 390/500 nm. Chromatograms obtained for each sample from these nine detection modes were integrated and separated into four molecular fractions: >40 kDa, 20–40 kDa, 10–20 kDa, and <10 kDa. To enhance analytical resolution and normalize the data, ratios were calculated from the areas of chromatographic peaks obtained for each detection mode. The results demonstrate the utility of these ratios in discriminating samples composed of HAs, melanoidins, and their mixtures, through principal component analysis (PCA). Low molecular weight fractions were found to be specific to melanoidins, while high molecular weight fractions were characteristic of HAs. For the detection modes specific to melanoidins, UV absorbance at 210, 254, and 280 nm were predominantly present in the numerators, with tryptophan-like fluorescence emissions in the denominators. Conversely, fluorescence emissions largely represented both numerators and denominators for HAs. This online method also enables the discrimination of pseudo-melanoidins, compounds revealing a nitrogen deficiency in their chemical structures.