In this paper, we aim to account for the partitioning of finite sized ions and electric double layer (EDL) overlapping effects on the electrostatics and hydrodynamics of soft nanofluidics by stablishing a modified Poisson-Boltzmann (MPB) equation enjoying mean field approach. The application of the present MPB equation enables us to describe the interaction between the steric effect and electrostatic repulsion of EDL ions due to permittivity difference of polyelectrolyte layer (PEL) and electrolyte solution. Utilizing the Debye-Hückel approximation pertinent to low surface potentials, we analytically derive the solutions of electric potential and velocity profiles of mixed electroosmotic and pressure driven flows in polyelectrolyte grafted nanotubes. As well, we theoretically predict the electrophoretic mobility of soft colloidal particles immersed in aqueous solutions of NaCl, KCl, NaMnO4 and LiIO3 in the presence of ion partitioning effect (IPE). For the case of larger surface potentials, the nonlinear governing equations of the problem are analyzed by finite difference method, and the accuracy of the numerical solutions are examined by verifying the results with existing experimental data. Moreover, we calculate three electrokinetically associated phenomena namely streaming potential, electroviscous effect and electro-chemo-mechanical energy conversion (ECMEC) efficiency through soft nanotube having constant surface potential/charge density. Then, we compare our results under the purview of the present MPB equation with those predicted by point-like charge modeling of ions. The essential findings of our investigation highlight the importance of accounting for IPE arising from the permittivity difference of PEL and bulk salt solution when high degrees of softness, charge density and thickness of the PEL are encountered in transport mechanism in soft nanofluidics. We also show that one of the most important consequences of IPE is several fold increase of electrophoretic mobility of soft particle and ECMEC efficiency of soft nanotube due to increasing the PEL-electrolyte permittivity difference. © 2018 Elsevier Ltd