This exploratory study investigated higher education student experiences on the effects and limitations of mobile inquiry-based and inquiry-based science learning applications. A total of 80 pre-service science and elementary school teachers from a public university in Turkey were recruited in the study using availability sampling. Participants were randomly assigned to one of two groups; one group participated in face-to-face inquiry-based learning (IBL) and the other participated in mobile inquiry-based learning (m-IBL). Data were collected using semi-structured interviews after 6 weeks of inquiry. Three main categories arose from the data analysis: the effects of m-IBL and IBL applications, problems encountered in the applications, and attitudes toward the application process. It was found that both IBL and m-IBL activities contributed to the meaningful learning of the science subjects, an understanding of scientific research, and the development of thinking skills, such as scientific process skills and problem-solving.