Electron–phonon interactions play a crucial role in nano-electronic device performance. As the accurate calculation of these interactions requires huge computational resources, reduction of this burden without losing accuracy poses an important challenge. Here, we investigate the electron–phonon interactions of nano-devices using two first-principles-based methods in numerically efficient manners. The first method is the Lowest Order Approximation (LOA) version of the computationally burdensome self-consistent Born approximation method. The LOA method incorporates the effect of each phonon mode on the electronic current perturbatively. In this work, we theoretically resolve the discrepancy between two conventional approaches of direct LOA calculation. To validate the correct approach, we compared its output with a completely different method (second method) named Special Thermal Displacement (STD) method. The STD method uses non-interacting transport calculation of the displaced atomic configuration of a device. We apply both methods to two thin-film nanodevices: 2D silicon junctionless FET and n-i-n FET. Both methods justify each other by providing similar results and exhibiting important quantum phenomena, such as phonon-assisted subthreshold swing degradation and tunneling.