With a national prevalence of 0.9%, Burundi is close to achieving UNAIDS’ 2025 targets. Despite this, different types of crises periodically disrupt its HIV health services. The community-based program EPIC measured the impact of the COVID-19 health crisis on people living with HIV (PLHIV) in Burundi in 2021. Specifically, it assessed ART interruption and associated factors since the beginning of the pandemic. The study questionnaire was administered to PLHIV in three cities between October and November 2021. Participants were recruited using convenience sampling. Logistic regression models helped identify factors associated with ART interruption. Of the 317 respondents, 37 (11.7%) reported interruption. The majority (79.2%) self-identified as belonging to key populations. Interruption was significantly associated with: fewer HIV medical follow-up visits (adjusted Odds Ratio, aOR = 7.80, p = 0.001) and forced HIV status disclosure (aOR = 4.10, p = 0.004). It was inversely associated with multi-month ART dispensing (aOR = 0.36, p = 0.017) since the beginning of the pandemic and the perception of not having been sufficiently informed by the HIV medical team about the risk of COVID-19 infection (aOR = 0.11, p < 0.001). Our results highlight the importance of multi-month ART dispensing, enhanced communication, and voluntary disclosure of one’s HIV status in preventing ART interruption in times of crises in Burundi.