Abstract In this paper, theoretical and numerical analyses of the properties of some complex semi-Lagrangian methods are performed to deal with the issues of the instability associated with the treatment of the nonlinear part of the forcing term. A class of semi-Lagrangian semi-implicit schemes is proposed using a modified TR-BDF2 method, which is the combination of the trapezoidal rule (TR) and the second-order backward differentiation formula (BDF2). The process used for the nonlinear term includes two stages as predictor and corrector in the trapezoidal method and one stage for the BDF2 method. For the treatment of the linear term, the implicit trapezoidal method is employed in the first step, the explicit trapezoidal method in the second step, and the implicit BDF2 method in the third step. The combination of these techniques leads to a family of schemes that has a large region of absolute stability, performs well for the purely oscillatory cases, and has good qualities in terms of accuracy and convergence. The use of the explicit method for the linear term in the second step makes the proposed class of schemes competitive in terms of efficiency compared to some well-known schemes that use two steps. Numerical experiments presented herein confirm that the proposed class of schemes performs well in terms of stability, accuracy, convergence, and efficiency in comparison with other, previously known, semi-Lagrangian semi-implicit schemes and semi-implicit predictor–corrector methods. The potential practical application of the proposed class of schemes to a weather prediction model or any other atmospheric model is not discussed and could be the subject of other forthcoming studies.