We show the thickness dependent transition from metallic conduction to tunneling in threedimensional (3D) Ag/Si/Ag nano-junctions through layer-by-layer electronic structure and quantum transport calculations. The transmission coefficients are calculated quantum mechanically within the framework of density functional theory in conjunction with non-equilibrium Green's function techniques. Thin junctions show nearly metallic character with no energy gap opening in Si layers due to the metal-induced interface states, and the transmission is independent of the stacking order of Si layers. Energy gap reemerges for Si layers deeply buried within thick junction, and the decay rate of transmission in this insulating region depends on the stacking order. Complex band analysis indicates that the decay of transmission is not determined by a single exponential constant but also depends on the available number of evanescent states. Calculating the electric resistance from the transmission coefficient requires a 3D generalization of the Landauer formula, which is not unique. We examine two approaches, the Landauer-Büttiker formula, with and without subtraction of the Sharvin resistance, and a semi-classical Boltzmann equation with boundary conditions defined by the transmission coefficients at the junction. We identify an empirical upper limit of ∼ 0.05 per channel in the transmission coefficient, below which the Landauer-Büttiker formula without the Sharvin resistance correction remains a good approximation. In the high transmission limit, the Landauer-Büttiker formula with Sharvin correction and the semi-classical Boltzmann method reach fair agreement.