Certain example embodiments relate to coated articles with sequentially activated low-E coatings, and/or methods of making the same. In certain example embodiments, one or more infrared reflecting layers is/are activated via a non-equilibrium preconditioning activation that uses photons with specific frequencies/frequency ranges, followed by a more equilibrium thermal activation. The preconditioning activation aids in rearranging the silver atoms to energetically favorable positions, while helping to avoid their unwanted agglomeration. The more equilibrium thermal stage of activation aids in aligning the chemical potentials of the layers of the stack and in further densification of the preconditioned silver layer. Doing so, in turn, helps to reduce the likelihood of stresses building-up in the coating, the formation of point and dimensional defects, other unwanted efficiency-reducing phenomena, and/or the like. Advantageously, emissivity can be lowered to a value lower than that achievable using conventional thermal, flash, and laser scanning, approaches alone.