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Undernutrition among HIV/AIDS patients impedes the achievement of sustainable development goals by placing additional strain on healthcare systems. HIV causes nutrient loss and malabsorption, increasing nutritional requirements, particularly in lactating women. HIV-infected breastfeeding mothers are at greater nutritional risk than their non-HIV counterparts. Although global studies have addressed maternal undernutrition, few in Uganda have focused on factors affecting nutrient intake and nutritional status among HIV-positive breastfeeding women. This study aimed to explore these factors in Apac District. A cross-sectional study involving 220 HIV-positive breastfeeding mothers was conducted. A pre-tested 24-hour recall questionnaire, using the dietary diversity score for women (DDS-W), was used to collect data. Nutritional status was assessed using body mass index (BMI), while nutrient intake was determined by entering actual intakes into an Excel sheet to calculate total nutrient intake per individual, from which mean nutrient intake and mean adequacy ratio (MAR) were calculated. Data were analysed using Stata version 15 at univariate, bivariate, and multivariate levels. The level of significance was set at 5%, with a 95% confidence interval; the null hypothesis was rejected when p-values were less than 0.05. A total of 10.6% of participants were undernourished, with a dietary diversity score of 4.3 food groups, while 21% had a poor dietary diversity score. Participants met 61% of their recommended micronutrient intake, with energy, lipid, zinc, calcium, and vitamins A, C, B6, and B12 intakes below recommendations. Factors associated with nutritional status included maternal age [AOR = 1.94, 95% CI (1.05–3.59)], presence of a market [AOR = 0.42, 95% CI (0.223–0.784)], means of obtaining food [AOR = 0.55, 95% CI (0.234–0.94)], and presence of cultural food taboos [AOR = 0.44, 95% CI (0.136–0.998)]. Factors associated with nutrient intake were presence of a market [p = 0.018, 95% CI (0.010–0.104)], income [p = 0.010, 95% CI (0.007–0.048)], DDS [p < 0.001, 95% CI (0.022–0.058)], and household head [p = 0.049, 95% CI (–0.095–0.001)]. There is a prevalence of undernutrition among HIV-positive breastfeeding mothers in Apac District, accompanied by poor dietary diversity scores and low micronutrient intake. Interventions to increase dietary diversity scores, provide nutrition education, and improve income should be promoted.