It is the intention of the current study to suggest a trajectory for the advancement of prospective mathematics teachers’ use of meta-cognitive skills in solving mathematics-based programming problems with Scratch. Scratch is a code-based program that can be utilized in teaching various disciplines, especially geometry and its rich range of subjects such as the topic of symmetry. The present study suggests that advancing prospective teachers’ meta-cognitive skills in the Scratch environment could be done through problem solving and negotiations. The present paper analyzed the implementation of the trajectory by two pedagogic supervisors who attempted, in the frame of one-year preparation (2018–2019), to educate 18 prospective teachers to use meta-cognitive skills in mathematics-based programming activities, where this attempt was based on problem solving and negotiation processes. Data were collected through videoing and recording the learning sessions of the prospective teachers and was analyzed using deductive and inductive constant comparison methods. The deductive analysis utilized theoretical models of meta-cognitive processes and negotiation processes. The research results indicated that the negotiation processes supported the development of the prospective teachers’ meta-cognitive processes in solving mathematics-based programming problems with Scratch.