The perception of the existence of deficits in patient safety, the associated costs and the limitation of resources have made it essential to define improvement strategies. Important concepts have emerged, such as safety climate, which evaluates the perceptions of safety status held by professionals in relation to their organization. The aim of this study is to characterize the safety climate in primary health care (PHC) using the Safety Attitudes Questionnaire (SAQ)—Short Form 2006 PT and to assess associations between SAQ-Short Form 2006 PT scores and demographic and professional characteristics. A cross-sectional study was conducted in all public PHC units in the northern region of Portugal. Data were collected through an online questionnaire shared via institutional emails and by means of a snowball approach. Descriptive and inferential statistical analysis were performed. Statistical significance set at p ≤ 0.05. A total of 649/7427 (8.7%) responses were included in the analyses. The mean and median total SAQ-Short Form 2006 PT scores were 69.23 (SD = 15.73, range 22.22–100.00) and 71.53 [59.03; 79.86], respectively. This is the first study to assess the safety climate in PHC in Portugal. The median obtained total SAQ-Short Form 2006 PT score was 71.53 [59.03; 79.86], which is below the threshold of ≥75, indicating safety deficits.