This study investigated if prospective secondary science teachers enhance their argumentation skills and the interaction of the change in their argumentation skills with their conceptual knowledge during an argumentation-based guided inquiry course. 37 prospective secondary science teachers constituted the study sample. They were grouped according to whether or not they had a misconception about understanding of balanced forces at the beginning of the course. They performed oral and written argumentation tasks during the course. Their written argumentation tasks were assessed four times during the course for balanced forces and sinking and floating behaviour of objects. Results indicated that prospective secondary science teachers developed mostly counter-argument and rebuttal skills. In addition, different trends of the change in argumentation skills were identified for prospective secondary science teachers having a misconception and those having a scientific conception. Implications for teacher education and science education were discussed according to these results.