Our objective was to estimate the prevalence and risk factors for long COVID symptoms among polymerase chain reaction–confirmed COVID-19 patients (hospitalised and community) in Malta. This was a national cross-sectional survey among COVID-19 patients in Malta during 2020. Patients were sent a questionnaire 3–6 months after testing positive. Data were analysed descriptively to estimate symptom prevalence, and multivariable logistic regressions were used to determine the risk factors for long COVID symptoms. Age, sex, initial symptoms, hospitalisation, and healthcare worker status were used as risk factors and symptoms (cough, shortness of breath, fatigue, anxiety, sadness, and memory loss) 2.5 months or more after COVID-19 onset were used as outcomes. Of 8446 eligible participants, 2665 (31.55%) responded with a median age of 37 years. Initial symptoms were reported in 82% of responders, and 7.73% were hospitalised. Among the long COVID symptoms, fatigue persisted among most non-hospitalised responders, whereas anxiety, shortness of breath, and sadness were the most common symptoms. Female sex, hospitalisation, and initial symptoms were associated with higher odds of fatigue, shortness of breath, cough, anxiety, sadness, and memory loss as long COVID symptoms. Our study is the first to highlight long COVID symptoms and risk factors in Malta, showing that long COVID is common among hospitalised and non-hospitalised patients. These data should increase awareness of long COVID and facilitate support to those affected nationally.