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.