We have performed detailed studies of the temperature evolution of the electronic structure in Ba(Fe(1-x)Ru(x))2As2 using Angle Resolved Photoemission Spectroscopy (ARPES). Surprisingly, we find that the binding energy of both hole and electron bands changes significantly with temperature in pure and Ru substituted samples. The hole and electron pockets are well nested at low temperature in unsubstituted (BaFe2As2) samples, which likely drives the spin density wave (SDW) and resulting antiferromagnetic order. Upon warming, this nesting is degraded as the hole pocket shrinks and the electron pocket expands. Our results demonstrate that the temperature dependent nesting may play an important role in driving the antiferromagnetic/paramagnetic phase transition.