Grape pomace (GP) has an added value because of its contribution to carbon (C) and nitrogen (N) in soils when applied as an organic fertilizer. Macronutrients from GP are translocated into the soil after amendment, but little is known about the factors that may influence the mobility of C, N and bioactive molecules, i.e., polyphenols, in the soil column. We investigated the mobility of the macronutrient content of GP, derived from two red (Dornfelder and Pinot noir) and two white grape varieties (Riesling and Pinot blanc). For that, three different soils (loamy sand RefeSol01A, silt loam RefeSol02A and a vineyard soil) were evaluated in a column model using a GP application rate of 30 t ha−1. The three-step lab-scale approach included the analysis of total C, N and polyphenols expressed as total polyphenolic content (TPC) in: (a) the fresh GP, representing the total amount of C, N and TPC; (b) the mobility with rainwater, representing the aqueous extractable fraction and (c) the mobility in the soil column and leaching potential. Our results showed that total C/N ratios were wider in the white GP varieties compared with the red ones. Higher TPC values were measured in Dornfelder and Pinot noir compared with white varieties. Analysis of the water-extractable fraction showed that the C recovery may reach up to 48% in Pinot blanc, which also corresponds to the highest N contribution. Extractable polyphenols were higher in the red compared with the white varieties by a factor of 2.4. C and N were mobilized with rainwater from the GP through the soil column. However, the application rate used in the experiment was not indicative of an accumulation in the soil. Compared with the control (no GP application), C values were significantly higher in the leachates from GP-treated soils, in contrast to N values. Up to 10% of the TPC of the pomace was leached into the soil. The TPC recovery in the soils strongly depended on the combination of soil type and GP variety. Generally, the sandy and more acidic soil showed an even distribution of phenolics with a high recovery rate (up to 92%) compared with more neutral and silty soil. Most of the polyphenol content could accumulate in the upper soil layer (0–10 cm). These results provide the first insights on the mobility of macronutrients in the soil using a column model and point out the need to relate those experiments to soil and GP properties in order to avoid the accumulation of nutrients in soil or mobility to adjacent ecosystems.