Thermoelectricity has been investigated mostly on the macroscopic scale despite the fact that its origin is linked to the local electronic band structure of materials. While the role of thermopower from microscopic structures (e.g., surfaces or grain boundaries) increases for emerging thermoelectric materials, manipulating thermoelectric puddles, spatially varying levels of thermoelectric power on the nanometer scale, remains unexplored. Here, we illustrate thermoelectric puddles that can be harnessed via the stacking order and electronic screening in graphene. The local thermoelectric elements were investigated by gate-tunable scanning thermoelectric microscopy on the atomic scale, revealing the roles of local lattice symmetry, impurity charge scatterings, and mechanical strains in the thermopower system. The long-range screening of electrons at the Dirac point in graphene, which could be reached by in-operando spectroscopy, allowed us to unveil distinct thermoelectric puddles in the graphene that are susceptible to the stacking order and external strain. Thus, manipulating thermoelectric puddles via a lattice symmetry and electronic engineering will realize practical thermopower systems with low-dimensional materials.