Learning to plan modeling-based investigations (MBIs) presents significant challenges for pre-service elementary teachers. Although they understand disciplinary core ideas and modeling practices, they address both as competing learning goals and, as novices, they have not experienced how to structure MBIs for their future students. In the context of a science teacher education course, we have designed a set of pedagogical supports around a biology-specific epistemic tool to help pre-service elementary teachers meet those challenges. This study builds the case of how a group of four pre-service elementary teachers learns to plan MBIs while working with the designed supports. We use the professional vision as a theoretical and analytical framework to characterize the group's learning through discourses to build shared professional understandings of planning MBIs around biology core ideas. Analysis focused on their highlighting and coding of relevant aspects of disciplinary core ideas, modeling, and structuring MBIs, as well as their creation and use of material representations. The findings illustrate that: a) epistemic negotiation supports the group in integrating biology core ideas and modeling practices when developing explanatory models, and b) pedagogical negotiation, through the de-construction of those explanatory models, supports the group structuring of a MBI, including a natural phenomenon and questions students can investigate in a coherent sequence. We discuss how a biology-specific epistemic tool embedded in pedagogical supports helps pre-service teachers learn to plan MBIs by facilitating both epistemic and pedagogical negotiations.