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First-year university students’ knowledge and conceptual understanding of general chemistry has been investigated using a multiple-choice concept inventory (Chemical Concept Inventory 3.0/CCI 3.0) as a pre-test (n = 221) and a post-test (n = 90) in two first-semester chemistry courses. This paper discusses the students’ answers to two questions about bond energy. Student interviews (n = 7) were performed for further insight in the students’ thought processes and validation of the CCI questions. Although many students appeared to recall that breaking a chemical bond demands energy, most were not able to use this fact to reason about the heat released in a chemical reaction, and the alternative conception that bond breaking releases energy seemed deeply ingrained and prevalent among the students. For one of the questions, more students gave the correct answer on the pre-test than on the post-test. Student interviews indicated that some students’ failure to pick the correct alternative for this question might be influenced by use of the word “always” in the correct answer, which discouraged those students that find chemistry to be a subject full of exceptions.