A novel algorithm to design hybrid waveguide-microstrip transversal microwave filters is proposed in this paper. The idea consists in isolating each resonator involved in the filter structure, to synthesize individually its frequency response, both in resonant frequency and bandwidth. These separated optimizations lead to the dimensions of the filtering structure to meet the requirements of a certain, specified transfer function. The novel algorithm introduces an iterative procedure in order to synthesize the direct coupling term between source and load, which is always present in the hybrid filter structure. The whole algorithm is illustrated by means of a design example, where a very good agreement between the ideal specified transfer function and the final frequency response of the designed hybrid filter is obtained. A second different design example, which has been manufactured and tested, is also included for validation.