In this study, we introduce the area efficient low complex runtime reconfigurable architecture design methodology based on Skyrmion logic for universal logic gate (ULG) i.e. NOR/NAND implementation using micromagnetic simulations. We have modelled the two input 3D device structure using bilayer ferromagnet/heavy metal where the magnetic tunnel junctions inject and detect the input and output skyrmions by exploiting the input reversal mechanism. The implementation of NOR and NAND is performed using this same device where it is reconfigured runtime with enhanced tunability by the ON and OFF state of current passing through a non magnetic metallic gate respectively. This gate acts as a barrier for skyrmion motion (additional control mechanism) to realize the required Skyrmion logic output states. To the best of authors’s knowledge the boolean optimizations and the mapping logic have been presented for the first time to demonstrate the functionalities of the NOR/NAND implementation. This proposed architecture design methodology of ULG leads to reduced device footprint with regard to the number of thin film structures proposed, low complexity in terms of fabrication and also providing runtime reconfigurability to reduce the number of physical designs to achieve all truth table entries (∼75% device footprint reduction). The proposed 3D ULG architecture design benefits from the miniaturization resulting in opening up a new perspective for magneto-logic devices. © 2023 IOP Publishing Ltd.