A project on developing a 2.45 GHz microwave ion source based compact ion implanter and plasma diagnostic facility has been taken up by the Central University of Punjab, Bathinda. It consists of a double-wall ECR plasma cavity, a four-step ridge waveguide, an extraction system, and an experimental beam chamber. The mechanical design has been carried out in such a way that both types of experiments, plasma diagnosis and ion implantation, can be easily accommodated simultaneously and separately. To optimize microwave coupling to the ECR plasma cavity, a four-step ridge waveguide is designed. Microwave coupling simulation for the ECR plasma cavity has been performed at different power inputs using COMSOL Multiphysics. An enhanced electric field profile has been obtained at the center of the ECR plasma cavity with the help of a four-step ridge waveguide compared to the WR284 waveguide. The magnetic field distribution for two magnetic rings and the extraction system’s focusing properties have been simulated using the computer simulation technique. A tunable axial magnetic field profile has been obtained with a two permanent magnetic ring arrangement. The dependency of the beam emittance and beam current on accelerating voltages up to 50 kV has been simulated with different ions. It shows that ion masses have a great impact on the beam emittance and output current. This facility has provision for in situ plasma diagnosis using a Langmuir probe and optical emission spectroscopy setups. This system will be used for ion implantation, surface patterning, and studies of basic plasma sciences.