This study compared the effect of the instructional treatments (guided inquiry-based and traditional recipe-like approach) and the learning environments (authentic and virtual learning environments) on pre-service science teachers’ understanding of chemistry concepts. For this purpose, Authentic Inquiry-based Laboratory, Virtual Inquiry-based Laboratory, Authentic Recipe-like Laboratory and Virtual Recipe-like Laboratory were designed. Eight laboratory activities related to thermochemistry, chemical kinetics, chemical equilibrium, acids and bases and electrochemistry were developed. Sixty-eight pre-service science teachers were randomly stratified into four equal groups: Authentic Inquiry-based Laboratory, Virtual Inquiry-based Laboratory, Virtual Recipe-like Laboratory and Authentic Recipe-like Laboratory. A two-tier General Chemistry Concept Test developed by researchers was used for the data collection tool before and after the treatment and data were analysed using nonparametric statistical methods. According to the results there was a significant difference between post test scores of groups and this difference was between Authentic Inquiry-based Laboratory and Authentic Recipe-like Laboratory, Virtual Inquiry-based Laboratory and Authentic Recipe-like Laboratory. Mean scores of groups were arranged from the highest to the least as Authentic Inquiry-based Laboratory, Virtual Inquiry-based Laboratory, Virtual Recipe-like Laboratory and Authentic Recipe-like Laboratory. Each item of the test was also analysed and changing of alternative conceptions was assessed. Decreasing of frequencies of alternative conceptions were generally arranged same as mean scores except for chemical kinetics.