To better understand the epizootiology of caprine paratuberculosis in the North of Portugal, a cross-sectional study was conducted from 2014 to 2015. The seroprevalence and risk factors for Mycobacterium avium subsp. paratuberculosis (Map) seropositivity were evaluated. Antibodies against Map were determined by a commercial ELISA. In 936 sera tested from 56 goat herds, 120 (12.8%, 95% CI: 10.8–15.1%) goats and 34 (60.7%, 95% CI: 47.6–72.4%) herds were positive. Risk factors for seropositivity were investigated by logistic regression models. The odds of Map seropositivity were found to be higher for animals with clinical signs, OR = 5.1 (95% CI: 2.7–9.6%), animals belonging to herds with previous wasting disease, OR = 2.3 (95% CI: 1.1–4.8%), and accumulation of manure in the herd, OR = 3.1 (95% CI: 1.7–5.7%). The potential risk factors identified in this study support the current recommendations for the control of paratuberculosis in these and other animals.