This paper presents the variation in natural frequencies of Euler-Bernoulli microbeams when subjected to axial pretension. The influence of size effects has been analysed using modified strain gradient theory (MSGT). The governing equation of motion has been derived using extended Hamilton’s principle and variational calculus. The sixth order non-local governing differential equation is solved by analytical procedure and numerical differential quadrature method (DQM). The three end conditions of beams are considered: cantilever, simply supported, and clamped-clamped beams. It is found that MSGT accurately models the size effects compared to other theories. As the axial pretension increases from 0.0001 to 1 N, the natural frequency values for the beam with different boundary conditions increase. Subsequently, surface elasticity effects have been analysed for a silicon and aluminium-based nanobeams with the pretension of 0.0001 N for all boundary conditions. From the results of surface elasticity modeling, it has been concluded that the natural frequencies of the nanobeam get influenced either positive or negative based on the value of surface elastic modulus. The difference in natural frequency values with and without surface elasticity effects are approximately 5 and 2% for Si and Al nanobeams respectively. The methodology presented in this work can further be validated for nanoscale devices in which the higher-order strain gradient and surface elasticity effects subjected to pretension dominate. © 2023, The Author(s), under exclusive license to Springer Nature Switzerland AG.