This article presents a qualitative study of the type and quality of questions formulated by prospective elementary teachers (PETs) when designing scientific inquiry activities, depending on the school science content selected. The data were acquired during teacher training instruction on these aspects with 67 participant PETs. The results showed that the PETs in general posit questions that are interesting, but not always conducive to starting some scientific inquiry in class. Within the set of high-order questions for inquiry (relating variables), it was found that those oriented to making predictions presented the most difficulties. The content the PETs selected to formulate questions covered a wide variety of topics or phenomena related to physics, chemistry, biology, and astronomy. The highest quality questions proposed in greater numbers were proposed in order to study Changes of State and Plants. Likewise, all the questions formulated about phenomena related to Flotation, Magnetism, and Gravity were of high order, while the poorest quality questions (not scientifically researchable) were related to the study of Machines. It was also found that the PETs frequently identified the variable with the object rather than with a property or magnitude. To conclude, some suggestions are made to improve teacher training with regard to inquiry-based science teaching and learning.