The purpose of this descriptive case study was to develop pre-service chemistry teachers’ Technological Pedagogical Science Knowledge (TPASK) through novel computational chemistry modules. The study consisted of two phases starting with designing a computational chemistry based learning environment followed by a case study where students’ perceptions towards educational computational chemistry were explored. First, we designed an authentic research-based chemistry learning module that supported problem-based learning through the utilisation of computational chemistry methods suitable for pre-service chemistry education. The objective of the learning module was to promote learning of specific chemistry knowledge and development of scientific skills. Systematic design decisions were made through the TPASK framework. The learning module was designed for a third-year physical chemistry course taken by pre-service chemistry teachers in Chile. After the design phase, the learning module was implemented in a course, and students’ perceptions were gathered using semi-structured group interviews. The sample consisted of 22 pre-service chemistry teachers. Data were analysed through qualitative content analysis using the same TPASK framework employed in the learning module design. Based on our findings, pre-service chemistry teachers first acquired Technological Scientific Knowledge (TSK) and then developed some elements of their TPASK. Besides, they highly appreciated the combination of student-centred problem-based learning and the use of computational chemistry tools. Students felt the educational computational learning environment supported their own knowledge acquisition and expressed an interest in applying similar learning environments in their future teaching careers. This case study demonstrates that learning through authentic real-world problems using educational computational methods offers great potential in supporting pre-service teachers’ instruction in the science of chemistry and pedagogy. For further research in the TPASK framework, we propose there would be significant benefit from developing new learning environments of this nature and evaluating their utility in pre-service and in-service chemistry teacher's education.