The development of two-dimensional chromatography systems is crucial in many scientific fields as it provides improved separation efficiency and selectivity of complex mixtures. By separating compounds based on two independent properties, these systems can offer a more detailed understanding of sample composition. This increased level of detail is particularly useful in industries such as pharmaceuticals, environmental analysis, and proteomics, where complex mixtures with similar properties need to be differentiated. A new chromatography system with two dimensions was developed to separate and quantify specific flavonoids in German wine samples. The first dimension used a homemade hydrophilic interaction liquid chromatographic column, while the second dimension used a reversed-phase liquid chromatographic column. This 2D ZIC-HILIC x RP technique was able to address the problem of peak overlapping that commonly occurs in one-dimensional liquid chromatography, especially for natural products. The study presents analytical and statistical data for both techniques, and suggests that the use of two-dimensional chromatography can improve the resolution of conventional one-dimensional liquid chromatography. In a conventional ZIC-HILIC-HPLC system, apigenin and naringenin were detected together but were successfully separated and measured using a 2DLC system. The limits of detection (LOD) for apigenin and naringenin were found to be 0.0705 µg/mL and 0.1300 µg/mL, respectively, while the limits of quantification (LOQ) were 0.2136 µg/mL and 0.3939 µg/mL, respectively. The recovery rate for both compounds was over 99%, with a relative standard deviation (RSD) of less than 1.5%. The linearity range for both compounds was between 0.005 µg/mL to 10 µg/mL, and the correlation coefficient (r2) was determined to be 0.9998. For hesperidin and rutin, the LOD and LOQ were found to be 0.0336 µg/mL and 0.1018 µg/mL, and 0.0120 µg/mL and 0.0363 µg/mL, respectively. The linearity range for both compounds was between 0.005 µg/mL to 12 µg/mL, and the correlation coefficient (r2) was determined to be 0.9999.