Purpose: The demand for Accounting Information Systems (AIS) knowledge has increased exponentially over the past two decades, but studying AIS has not proved easy for many accounting students. The aim of the study is to understand the challenges accounting students face in studying AIS through investigation of the factors which may be contributing to their difficulties. Design/methodology/approach: A survey instrument was developed for this study, and data were gathered from 618 students enrolled in AIS courses, 95 per cent of whom were accounting students. The data were analysed using Structural Equation Modelling (SEM) with the Partial Least Squares (PLS) technique. Findings: The results show that course structure, pre-existing knowledge of Information Systems (IS), assessment of critical thinking, teaching style and the availability of academic assistance to students all have a significant influence on students' learning experience in AIS courses. Research limitations/implications: The study has important implications for AIS educators through its identification and analysis of possible difficulties faced by students. It is hoped that remedial measures to enhance this experience will be explored and implemented. Practical implications: The study was conducted in one university context, so caution should be exercised in generalising the results. Future research could further validate, question, or extend the findings in multiple tertiary education institutions, in various countries. Originality/value: This is one of the first studies to introduce scales to measure students' perceptions and experiences in AIS courses. It is hoped that this paper will initiate a discussion that leads to a better understanding of students' perceptions of challenges, and thus make AIS learning a richer and more enjoyable experience for students.