Mechanistic reasoning is a critical thinking skill in science disciplines like chemistry because it helps students understand the entities and activities driving mechanisms. Given the complex interplay of the involved entities and the occurring activities, explicitly guiding students to explain why mechanisms occur can advance their mechanistic reasoning. Nonetheless, encouraging students not only to explain why a mechanism is plausible but also why related ones may be rather implausible might further enhance their mechanistic reasoning. This study compares the complexity of undergraduate organic chemistry students’ mechanistic reasoning when judging the plausibility of alternative mechanisms using quantitative analyses. The findings reveal certain characteristics that contribute to a higher mechanistic reasoning complexity, with the initial claim about whether a mechanism is plausible or implausible being a central predictor of students’ mechanistic reasoning complexity. Considering these findings, supporting students’ claim-making can be a first step in advancing their mechanistic reasoning. From a broader perspective, such support can highlight that specific interpretations of mechanistic outcomes allow for a certain degree of ambiguity, which provides transferable implications to other science disciplines.