Co-elution is a common challenge in phytochemical chromatography. Full chromatographic separation often requires extensive optimization, long analysis times, and excessive solvent use. A viable alternative could be mathematical elution of analytes using three-dimensional decomposition. This study aimed to develop a method to determine chlorogenic acid in Melampyrum stenophyllum Boiss. extracts without complete chromatographic separation, to validate the method, and to cross-validate assay results against a classical ultra-performance liquid chromatography (UPLC) method. Ultra-performance liquid chromatography-photodiode array (UPLC-PDA) spectrochromatograms were arranged into a three-way data cube with dimensions of time, wavelength, and sample and then decomposed using parallel factor analysis to reveal chromatographic, spectral, and concentration profiles. The chromatographic and spectral profiles were used to identify chlorogenic acid in overlapping signals. The relative concentration profile was used to quantify it in the plant extract. The assay results were statistically compared with those from an in-house classical UPLC method. Chlorogenic acid was co-eluted at 1.45 min and quantified as 16.11 mg per gram dry weight of Melampyrum stenophyllum extracts (SD = 0.28), despite significant interference in a 4-min runtime. The analytical validity was confirmed by recovery calculations from standard solutions and standard addition samples (RSD < 2%), and the t-test resulted in a p-value of 0.09 (α = 0.05), indicating no significant difference between the results obtained from mathematical elution and chromatographic separation. Chlorogenic acid was quantified from plant material accurately despite the co-elution. Validation and cross-validation results support the method's applicability.