A common practice amongst scientists is to evaluate the connections between evidence and claims about natural and human-induced phenomena. Teacher education coursework may improve understanding of this important activity and facilitate teachers to implement evidential thinking approaches into their future science teaching. Instructional scaffolds that actively engage students in scientific evaluation can be introduced in teacher education programs to increase pre-service teachers' understanding of critical evaluation as a scientific practice. The purpose of this qualitative exploratory study was to investigate pre-service science teachers' critical evaluation and decision-making practices using scientific evidence to consider competing, alternative explanations about controversial phenomena (genetically modified organisms and climate change). In this context, we analyzed pre-service science teachers' evaluations about the connections between scientific evidence and alternative explanations, as well as their decision-making practices by examining their certainty and plausibility judgments. Our findings indicated that participants' associations between evidence and explanatory models, their evaluative reasoning practices, and the correctness and complexity of their evaluations revealed variations in both topics. The participants' evaluation and decision-making practices also showed disputes with their plausibility judgments about alternative explanations, as well as the certainty of their evaluations. The findings were discussed in the light of the literature and suggested that critical evaluation is a scientific practice that should be explicitly taught in teacher education programs to increase pre-service science teachers' engagement and understanding of evidence-based decision-making practices.