This study analyzes the potential of group-based negotiation processes based on changes in reasoning and argument weighting for a socioscientific issue (SSI) in biology classes. In the corresponding pre- and post-study, students were encouraged to reason and weight arguments about the conservation of local biodiversity before and after a group-based negotiation. For this purpose, the students employed a target-mat structuring tool for compensatory reasoning and weighting in both the individual pre- and post-phases and the group phase. To identify changes in reasoning after group-based negotiation, the use of argumentative resources, i.e., fact-based and normative resources, was assessed. When the students added confirming reasons for arguments, they were more likely to use fact-based resources. When refuting the initial reasoning, the students tended to add normative resources. Furthermore, individual changes in weightings and their relationship to the group weighting were calculated. This analysis revealed that the students changed their weightings toward the group weighting. The results are discussed in terms of the potential of negotiations to cause students to revise and rethink their reasoning and weighting in addressing SSIs and the particular potential of the target-mat instructional tool for structured decision-making.