The Generalized Uncertainty Principle (GUP) has been discussed in the thick braneworld scenario. By considering Rydberg atoms in this background, we show that the spacetime geometry affects Maxwell equations inducing an effective dielectric constant on the space. In its turn, the corrected Coulomb potential by the gravitational interaction yields a deviation on the 3-dimensional Bohr radius. Then, we compute the corrections on the fine structure constant owing to the GUP in higher-dimensional spacetime. We also found constraints for the deformation parameter beta and D-dimensional Planck length l_{D} by comparing the predicted deviations with the recent empirical data of the fine structure constant. We compute the intermediate length scale, which in principle may be larger than the Planck length scale. It is conjectured that below such scale Quantum Gravity effects should take place.