In this work we have studied the importance of thermal effects on the structural and transport properties of Ag atomic-size nanowires (NWs) generated by mechanical stretching. Our study involve time-resolved atomic high resolution transmission electron microscopy imaging and quantum conductance measurement using an ultra-high-vacuum mechanically controllable break junction combined with quantum transport calculations. We have observed drastic changes in conductance and structural properties of Ag NWs generated at different temperatures (150 and 300 K). By combining electron microscopy images, electronic transport measurements and theoretical modeling, we have been able to establish a consistent correlation between the conductance and structural properties of Ag NWs. In particular, our study has revealed the formation of metastable rectangular rod-like Ag wires along the  crystallographic direction.