Objective The objective is to compare the clinical and laboratory characteristics of systemic lupus erythematosus (SLE) patients with and without lupus enteritis (LE) and to identify the factors associated with the occurrence of LE. Methods We performed a retrospective, case-control study in hospitalized patients with SLE who were admitted to our tertiary hospital between January 2012 and December 2021. Sixteen LE patients (cases) were matched (1:3 ratio) for sex and birth year with 48 non-LE patients (controls). Univariable and multivariable logistic regression analyses were used to identify the variables associated with LE. Results Of 2,479 SLE patients who were admitted to our hospital as inpatients, 16 (0.65%) were diagnosed as having LE. All patients, cases and controls, were of Mestizo ethnicity. SLE was diagnosed simultaneously with the first episode of LE in 10 (62.5%) patients. The median time from SLE diagnosis to the first episode of LE was 7 (IQR 0–78) months. LE patients had a shorter median disease duration [7 (0–78) vs 34 (9.5–79) months], and a significantly longer hospital stay (28.3 ± 15.8 vs 6.5 ± 7.9 days, p < 0.001) than non-LE patients. Most LE patients (93.8%) had concomitant lupus nephritis. LE patients had higher SLEDAI-2K scores than those without LE (20.5 ± 9.4 vs 9.8 ± 10.4, p < 0.001). By multivariable analysis, a higher SLEDAI-2K score (OR 1.10, 95% CI 1.02–1.18; p = 0.015) was independently associated with LE occurrence after adjusting for cutaneous involvement, lymphocyte count, serum creatinine, and serum complement C4. Recurrence was observed in two patients (12.5%), both with a bowel wall thickening > 8 mm. The two patients with large intestine-dominant LE developed intestinal pseudo-obstruction. No patient had life-threatening complications (intestinal hemorrhage, infarction, or perforation), and there were no deaths induced directly by LE itself. Conclusion In patients of Mestizo ethnicity, LE occurs during the early course of SLE, frequently is one of the presenting manifestations of SLE, and in most cases, it presents with concomitant lupus nephritis. Higher levels of disease activity at diagnosis were independently associated with LE occurrence and when recurrences occur, they do so in the context of severe wall thickness.