Suicide remains a major public health problem, with nearly 1 million deaths per year. The number tends to increase over time and factors leading to suicide suicidal behaviors are complex. However, there is a paucity of evidence on suicidal behaviors and the associated factors among people living with HIV (PLWH) in Indonesia. Therefore, this study aimed to estimate the prevalence and associated factors of suicidal behavior between indigenous and non-indigenous living with HIV who were on Dolutegravir and Efavirenz therapies. The cross-sectional data were collected using questionnaires. Participants completed the Suicidal Behaviors Questionnaire-Revised (SBQ-R), Depression Anxiety Stress Scale-42 (DASS-42), HIV Stigma-Sowell Scale, and demographic information questions. The outcome was low and high self-reported suicidal behaviors, while logistic regression analyses were used to estimate adjusted odds ratios (aOR) for associated factors of high suicidal behaviors. A total of 200 PLWH were enrolled and 8.5% of the participants had high levels of suicidal behaviors. The majority of participants were Efavirenz users (84.0%), and Papuans as Indigenous (75.5%). More than half had a high school education (60.5%), were female (58%), married (54%), and unpaid (59%). The multiple logistic regression model showed that indigenous (aOR = 0.122; 95% CI = 0.029–0.514), and people who had children (aOR = 0.221; 95% CI = 0.051–0.957) were more likely to have low suicidal behaviors. Participants who were aged 18–27 years (aOR = 5.894; 95% CI = 1.336–30.579), had high self-blame (aOR = 1.342; 95% CI) = 1.004–1.792), and detectable HIV viral load (aOR = 6.177; 95%CI = 1.118–34.119) had high suicidal behavior. This study identified the risk of suicidality among PLWHs is high and routine suicide assessment is prioritized. The findings are also useful for intervention design and the development of clinical practice guidelines to manage the well-being of PLWH such as using digital intervention to cope with hindrances.