<p>The ability to generate scientific investigative questions is a fundamental scientific practice that drives the exploration and understanding of natural phenomena. However, preservice and in-service primary school teachers have likely not had opportunities to learn how to generate investigative questions, especially in ways that integrate the big ideas of science and crosscutting concepts as called for by new reforms. We investigated primary preservice teachers’ (PSTs) abilities to engage in the science practice of asking investigation questions prior to taking science content courses. In this study, we considered how different phenomenon, and scaffolded prompts might relate to the quality of the PSTs’ investigative questions. We analyzed the responses of primary PSTs to a questionnaire in which they were asked to formulate investigative questions using the Crosscutting Concepts (CCCs) in response to three distinct scenarios, each involving a different phenomenon. We used three different versions of prompts within the questionnaire that could provide different types of scaffolding including problematizing and structuring in generating investigative questions. Through a series of chi-square tests, the findings revealed several significant associations, showing relationships between the quality of investigative questions posed by the PSTs with different phenomenon and scaffolded prompts. The findings also showed the PSTs often wrote accurate, aligned, and age-appropriate questions, yet the majority of the PSTs investigative questions would not lead to a systematic data collection as written. The analyses have implications for instructional strategies, curriculum design, and teacher training programs to support three dimensional science learning.</p>