Background: Depression and anxiety are prevalent among patients with systemic lupus erythematosus (SLE), and gut microbiota may be a contributing factor. This study aimed to investigate the clinical characteristics, food intake, and gut microbiota profiles of SLE patients with anxiety or depression. Methods: An analysis of secondary data was conducted. The primary study was conducted at Cipto Mangunkusumo Hospital, Jakarta, Indonesia, in 2017–2018. The inclusion criteria were: a diagnosis of SLE, age 18‒60 years, and gastrointestinal symptoms. The data collected included clinical data, food intake, anxiety and depression scores, SLE disease activity, and stool samples. Sequencing of the 16S rRNA gene was performed to profile the gut microbiota using DNA extracted from the stool samples. Results: After excluding those with incomplete data, 41 patients were analyzed. Among the subjects, 53.66% and 14.63% had anxiety and depression, respectively. SLE patients with anxiety were significantly more likely to harbor Bacteroides compared to those without anxiety (33.45% vs. 9.78%; p=0.02) and had lower levels of complement C3 (78.72 vs. 100.85 mg/dL; p=0.03). SLE patients with anxiety or depression had significantly lower fat intake compared to those without these conditions (38.78 vs. 48.43 g/day; p=0.04, and 31.48 vs. 45.27 g/day; p=0.04). A significant correlation was observed between the proportion of Bacteroides and SLE disease activity (p=0.02). Conclusion: SLE patients with anxiety showed a significantly higher proportion of Bacteroides and a lower C3 level compared to those without anxiety. Fat intake was significantly lower among SLE patients with anxiety or depression compared to those without either condition. © 2025, Indonesian Society of Internal Medicine. All rights reserved.