Background Cardiac arrhythmias, mainly atrial fibrillation (AF), is frequently reported in COVID-19 patients, yet causality has not been explored. Intensive Care Unit patients frequently present AF during critical illness. Sepsis is one of the main contributors of AF occurrence in ICU patients. The aim of the study was to explore if Covid-19 myocardial involvement is the only contributor for New Onset Atrial Fibrillation (NOAF) in intubated ICU patients. Methods Consecutive intubated, Covid-19ARDS patients, were prospectively studied for factors triggering NOAF. Demographics, data on Covid-19 infection duration, severity of illness and ARDS are reported. Echocardiographic findings, troponin levels and secondary infection (sepsis/septic shock) data were collected on the day of AF and compared to the preceding days’ and/or ICU admission data. Comparison was also performed between NOAF and control group (no AF) on admission. Results Among 105 patients screened, 79 were eligible; nineteen presented NOAF (24%). Baseline characteristics did not differ between the NOAF and control groups. Troponin levels were mildly elevated upon ICU admission in both groups. NOAF occurred on the 18 ± 4.8 days from Covid-19 symptoms’ onset, and the 8.5 ± 2.1 ICU day. Seventeen patients in the NOAF group (89.5%) presented a septic secondary infection vs 25 (41.6%) in the control group (p < 0.001). In sixteen NOAF patients (84.2%), AF occurred concurrently with a secondary septic episode. Noradrenaline, lactate levels and inflammation biomarkers presented a gradual increase in the days preceding the AF day (all p < 0.05). Troponin increased compared to admission (p = 0.017). AF did not resolve or re-occurred if sepsis persisted. Upon ICU admission left ventricular ejection fraction was rather normal, yet, global longitudinal strain was equally impaired (< 16.5%) in 63% vs 78% in the NOAF and control groups, respectively. The right ventricle was mildly dilated, and 36 (45.6%) patients had pericardial effusion. Echocardiographic findings did not change on NOAF occurrence. Conclusion Secondary infections seem to be major contributors for NOAF in Covid-19 patients, probably playing the role of the “second hit” in an affected myocardium from Covid-19.