The structural, microstructural, magnetic and electrical transport properties have been correlatively studied to decipher the complex consequences of variation of intrinsic parameter ,the average La-site cationic radii and extrinsic particle size on the magneto-electrical phase coexistence in La1-x-yPryCaxMnO3 (y = 0.30, 0.35, 0.40; x = 0.40). Polycrystalline powders prepared by sol-gel route were sintered at 600 °C, 900 °C, 1100 °C, and 1300 °C to facilitate particle size variation. Rietveld refinement of the powder X-ray diffraction data confirms that all samples have an orthorhombic structure with Pnma space group. The lattice constants decrease with decreasing ionic radii, while at a fixed ionic radius, the enhanced particle size increases them. The average apical Mn−O−Mn bond angles and the average Mn−O bond lengths decrease with rising ionic radii but increase with particle size at a fixed composition. Magnetization measurements show sequential paramagnetic (PM)-antiferromagnetic (AFM)-ferromagnetic (FM) transitions on lowering the temperature is lowered. The AFM-FM transition exhibits (i) pronounced hysteresis between field-cooled cooling (FCC) and field-cooled warming (FCW) (ii) strong divergence between zero-field cooling (ZFC) and FCW curves. The low-temperature magnetic state transforms from spin glass-like to a cluster glass-like as the ionic radii or the particle size decreases. These behaviors are caused by the mesoscale modifications in the magnetic phase profile where the AFM and FM phases due to the interplay between the average La-site cationic radii and the particle size. In general, the FM component increases with an increase in the particle size, but it decreases at lower ionic radii. The presence of a large thermal hysteresis in the insulator-metal transition (IMT) coupled with the one in FCC-FCW magnetization at particle sizes ~200 nm–160 nm, and ~460-400 nm demonstrates that this particle size regime is the most conducive to the phase separation. IMT disappears at smaller ionic radii and larger particle sizes due to the enhancement of AFM and charge-ordering. The PM and AFM regimes in all samples reveal variable range hopping conduction with particle size and ionic radii dependent activation. The observed phenomena have been explained in terms of the interplay between the ionic radii and particle size induced changes in the average apical Mn−O−Mn bond angles and the average Mn−O bond length.