A comparative study of the crystal structures and electrochemical characteristics of bulk and nanoscale La1-xPrxCoO3 (x = 0, 0.3 and 0.6) perovskites is made using synchrotron x-ray diffraction, cyclic voltammetry, and galvanostatic charge/discharge methods. It is shown that the sol-gel synthesized nano structures and bulk LaCoO3 exhibit different crystal structures, viz., rhombohedral [a = b = 5.4401 Å, c = 13.134 Å (on hexagonal axes), Z = 6, R3‾c] and monoclinic [am = 5.3865 Å, bm = 5.4482 Å, cm = 7.6365 Å, βm = 89.010°, Z = 4, I2/a], respectively. The evidence for CoO6 octahedra distortion in bulk LaCoO3 is also gathered from the three distinct Raman active modes at 518, 646, and 688 cm−1 emerging due to the Jahn-Teller effect, which, in-turn, reduces the crystal symmetry for achieving structure stabilization. This amounts to changes in Co–O bond lengths and Co–O–Co bond angles with promotion of t2g electron to eg level simultaneously for Co3+(3d6) to attain an intermediate spin state (S = 1) or higher. However, Pr-insertion induces phase transition to orthorhombic in both but with space group Pnma in nanostructures and equivalent Pbnm in bulk. The substitution effect on the specific capacitance (C) is opposite in nature, i.e., while ‘C’ decreases from 149 to 12 F/g in nano structures, it increases from 0.4 to 4 F/g in bulk with increase in Pr-content from x=0 to 0.6. A galvanostatic charge-discharge test of pristine nano LaCoO3 performed at a constant scan rate of 50 mVs−1 reveals electrode electrochemical stability by retaining 96 % of specific capacitance ∼82.5 F/g for 2000 cycles at least. The variation in the crystal structure and bond length and/or angle plays a key role in controlling the electrochemical performance of Pr-substituted LaCoO3 perovskites.