Organic chemistry has the long-standing reputation as a challenging course, and organic synthesis is an aspect of organic chemistry that requires students to make the most links between concepts and requires the highest order of thinking. One-on-one interviews were conducted with students from a second undergraduate organic chemistry course in which participants solved synthesis problems using a think aloud protocol. Those problems had been previously designed to scaffold students' acquisition of synthesis problem-solving skills. The research question for this study asked whether students worked through the synthesis learning activities as designed, toward the intended learning outcomes. The results show that in some questions, students used or tried to use desirable problem solving skills, such as using reaction mechanisms and chemical principles to explore possible solutions. However, with other question types, students (i) relied on familiarity with the reactions in question and lacked a problem-solving strategy when they could not recall the answer or (ii) avoided the purpose of the question and attempted to provide an answer that the professor “wanted.” Strategies for promoting desired synthesis skills and addressing other issues are discussed.