Background: The sudden shift by higher education institutions (HEIs) to emergency remote teaching (ERT), driven by the coronavirus disease 2019 (COVID-19) pandemic, pushed academic advisors of HEIs to suddenly shift towards e-academic advising to continue with the provision of academic advisory support services. However, few studies have concentrated on e-academic advising innovation challenges in the context of developing countries.Objectives: Therefore, the objective of this study was to examine students’ challenges in the innovative e-academic advising during ERT in a HEI in South Africa.Method: The study employed an online survey method and a stratified random sampling technique to select 240 first-year university undergraduate students from six faculties for the study. Structural equation modelling (SEM) with post hoc analysis, Bonferroni correlation, factor analysis with promax rotation and the Kaiser–Meyer–Olkin measure of sampling adequacy were employed in analysing the collected data.Results: The findings revealed significantly correlated institutional, technological and personal challenges to e-academic advising. Despite e-academic advising challenges being experienced differently across faculties, findings revealed that students experienced personal challenges more than institutional and technological challenges.Conclusion: Personal challenges are the most important factors for consideration when innovating to e-academic advising. The study concludes that the management of the HEI studied could improve the success of its innovation of integrating e-academic advising solutions to its academic affairs by considering a holistic approach that recognises the multifaceted challenges identified.Contribution: The study contributes to the discussion on student success in online learning environments. Once the challenges are identified, measures can be put in place to address them.