We investigate phase stability, microstructure, and thermoelectric transport of polycrystalline bulk Ca3−xRxMn2O7 samples prepared by standard solid‐state reaction, where R = Y or La and 0 ≤ x ≤ 0.33. Ab‐initio calculations predict that Y‐doping at Ca‐sites should reduce the potential energy barrier for electron transport, as opposed to La‐doping. We find that Y‐doping prompts transformation from Ca3Mn2O7 to Ca2MnO4, whereas La‐doping is accompanied by no phase transformation. La‐doping significantly hinders grain growth, for example, the average grain size decreases from 4.44 ± 0.24 to 1.20 ± 0.03 μm for x = 0 (undoped) and x = 0.33 upon La‐doping, respectively. Electrical conductivity and Seebeck coefficients are measured for the temperature range of 300–1300 K, and analyzed in terms of the small polaron hopping model. We find that Y‐doping reduces the activation energy for conduction compared to La‐doping, for example, 43 and 63 meV, respectively. This suggests that Y reduces the energy barrier for polaron transport, in accordance with computational predictions. This trend is further supported by calculations of selected electronic, structural, and vibrational properties, highlighting the intriguing correlation between electronic transport governed by small polarons and elastic properties, thereby shedding light on charge transport and thermoelectric properties of such layered perovskites.