Background Gut microbial translocation and increased intestinal barrier permeability are significant contributors to inflammatory non-AIDS co-morbidities in people living with HIV (PLWH). However, daily variations of markers of bacterial and fungal translocation along with intestinal damage are not characterized yet. Herein, we assessed the variation of these markers over 24 hours in PLWH receiving antiretroviral therapy (ART) in a well-controlled environment. Methods A total of 11 male ART-treated PLWH were recruited for the study. Blood samples were collected every 4 hours over 24 hours before snacks/meals from 8:00 in the morning to 8:00 the next day. All participants consumed similar meals at set times, and had a comparable amount of sleep, physical exercise and light exposure. Plasma levels of bacterial lipopolysaccharide (LPS) and fungal (1→3)-β-D-Glucan (BDG) translocation markers, along with markers of intestinal damage fatty acid binding protein (I-FABP) and regenerating islet-derived protein-3α (REG3α) were assessed by ELISA or the fungitell assay. Results Plasma levels of BDG and REG3α were stable during the day. In contrast, plasma levels of LPS and I-FABP were subject to daily variations, with the lowest levels at 12:00 and 16:00, respectively, and the highest levels at 00:00 and 4:00-8:00, respectively. Conclusions Conversely to the fungal translocation marker BDG and the gut damage marker REG3α, time of blood collection matters for the proper evaluation for LPS and I-FABP as markers for the risk of inflammatory non-AIDS co-morbidities. These insights are instrumental for orienting clinical investigations in PLWH.