Leptospirosis is one of the world’s major neglected tropical zoonotic diseases (NTZDs), implicated in animal health and welfare with economic consequences for livestock production. This study aims to estimate the seroprevalence of Leptospira spp. and identify potential risk factors in small ruminant herds. This epidemiological cross-sectional study was conducted in Nuevo León, a semi-arid region of Mexico. A total of 389 blood samples from goats and 385 from sheep older than eight months were randomly collected from 128 herds. Anti-Leptospira antibodies were detected using the microscopic agglutination test (MAT), and univariate and multivariate logistic regression analyses were performed to determine their association with leptospirosis infection. The overall prevalence was 13.5% (105/774), with 14.4% (56/389) in goats and 12.7% (49/385) in sheep. Sejroe was the most predominant serogroup. The main risk factors in sheep were contact with domestic cattle, ≥100 animals per herd, congenital abnormalities, contact with feral pigs, meat production system, absence of veterinary care, and abortions with odds ratios (OR) between 1.7 and 4.1. In goats, the main risk factors included lack of quarantine measures, contact with feral pigs, absence of veterinary care, and abortions where the OR ranged from 1.7 to 3.3. These findings indicate that Leptospira spp. is present in small ruminant herds. This is the first study aimed at understanding leptospirosis epidemiology in the northeastern region of Mexico, as goats and sheep may act as potential reservoirs. Continuous monitoring of Leptospira infections is imperative, as well as developing educational initiatives for farmers to implement biosecurity and prevention measures to prevent infections within herds and protect public health.