A retrospective cross-sectional study in 10 Croatian family medicine clinics included 1423 patients (58.0% female, mean age 52.6 ± 17.2 years), of which 82.4% had confirmed SARS-CoV-2 infection and 32.3% were unvaccinated. 28.1% of the participants had at least one chronic disease. The most common conditions after COVID were brain fog (4.9%), neurological disorders (4.7%), cardiovascular disease (2.9%), shortness of breath (2.8%), obesity (2.7%), and mental health disorders (2.6%). Higher severity of COVID-19 was associated with lung disease (β = 0.22; p = 0.031), age 51–65 years (β = 0.31; p < 0.001) and ≥66 years (β = 0.50; p < 0.001), while vaccination led to a milder course (β = -0.21; p < 0.001). Previous cardiovascular and musculoskeletal diseases increased the risk of thromboembolism, diabetes, obesity and number of vaccine doses predicted brain fog, neurological comorbidities of mental health disorders. The study highlights the importance of primary care in the early recognition and management of post-COVID conditions.