Toxoplasma gondii infection is relevant to animal production, food safety, and public health, but current epidemiological data for small ruminants in northeastern Portugal are limited. This cross-sectional study estimated seroprevalence and investigated factors associated with seropositivity in 2678 animals from 149 flocks sampled between May 2022 and December 2024. Serum samples were tested using an indirect enzyme-linked immunosorbent assay, and associated factors were evaluated using mixed-effects logistic regression with flock as a random effect. The overall true seroprevalence was estimated at 21.5% (apparent seroprevalence: 21.6%). At the flock level, 83.9% (125/149) of the sampled flocks were seropositive. True seroprevalence was higher in sheep than in goats (23.4% versus 14.4%), and seropositivity was detected in all surveyed municipalities. In the multivariable model, higher odds of seropositivity were observed in sheep (adjusted odds ratio 1.74), adult animals (2.78), non-native breeds (1.84), animals not kept in permanent housing (3.16), and animals from farms with cats (1.69). These findings indicate exposure throughout the surveyed area and associations with both host-related and farm-level characteristics. Strengthening farm biosecurity, limiting contamination of feed and water, and integrating animal health, environmental, and food safety measures may contribute to prevention within a One Health framework.