Purpose: During medical residency programs, physicians develop their professional identities as specialists and encounter high expectations in terms of achieving competencies. The responsibilities of medical trainees include caring for patients, balancing work with personal life, and weathering stress, depression, and burnout. Formal academic mentoring programs strive to ease these burdens. The coronavirus disease 2019 (COVID-19) pandemic has altered the trainee–academic mentor relationship, and solutions are needed to address these challenges. The present study aimed to evaluate the formal academic mentoring process through trainees’ perceptions and expectations of formal mentoring programs during COVID-19 in Indonesian cardiology residency programs.Methods: This cross-sectional study used a self-administered online questionnaire to capture trainees’ perceptions and expectations regarding academic mentoring programs in 3 cardiology residency programs in Indonesia from October to November 2020. The questionnaire was developed before data collection. Perceptions of the existing mentoring programs were compared with expectations.Results: Responses were gathered from 169 out of 174 residents (response rate, 97.3%). Most trainees reported having direct contact with COVID-19 patients (88.82%). They stated that changes had taken place in the mode and frequency of communication with their academic advisors during the pandemic. Significant differences were found between trainees’ perceptions of the existing mentoring programs and their expectations for academic mentoring programs (P<0.001).Conclusion: Despite the challenges of interacting with their academic mentors, trainees still perceived academic mentors as a vital resource. Study programs need to consider trainees’ expectations when designing academic mentoring programs.