The n=2 Ruddlesden-Popper Ca₃Mn₂O₇ exhibits several unusual properties including negative uniaxial thermal expansion and a complex domain structure and phase transition sequence. These properties can be tied to a polar/non-polar phase coexistence, however little is known about the atomic-scale structure of the phase coexistence or the underlying mechanism driving its formation. We combine electron microscopy measurements with density functional theory (DFT) calculations to directly image and understand the origin of coexisting polar and non-polar phases in Ca_2.9Sr_0.1Mn₂O₇ single crystals. At room temperature, we find that the atomic-scale structure of Ca_2.9Sr_0.1Mn₂O₇ consists of polar nano-phase regions of A2₁am symmetry embedded in a non-polar Acaa-symmetry matrix. Combining measurements of the local chemical environment with DFT calculations, we find that the polar nano-phase regions are stabilized by the substitution of Mn²⁺ dopants for some Ca²⁺ cations. Our calculations also show that it is energetically favorable for the Mn²⁺ dopants to cluster in a single rocksalt layer. These results provide insight into strategies to manipulate polar/non-polar phase coexistence and its associated properties.