One common notion is that all classrooms using Process Oriented Guided Inquiry Learning (POGIL) are the same. Though POGIL has essential components, this research found that students’ conceptual achievement, a classroom outcome, can be differentially affected by professors’ style of POGIL implementation. Audio/video recordings of student groups interacting during POGIL classes were analyzed, and these interactions were coded and characterized using two methods of coding. One involved phases and bridges of student interactions and the other examined students’ patterns of argumentation based on the Toulmin model of argumentation. As a result, differences in student outcomes between POGIL sections are explained as being influenced by nuanced ways professors interacted with groups during classroom instruction.