Background: Subjects with heart failure (HF) are at higher risk of developing thrombosis. We investigated whether endothelium activation and inflammation induce a prothrombotic biological profile in patients with acute decompensated HF (ADHF) and sinus rhythm. Methods: Our prospective study included 34 ADHF patients, 30 patients with stable chronic HF (CHF) and 30 control inpatients without HF. In vitro thrombin generation and its downregulation by activated protein C (APC) was monitored by calibrated automated thrombography at hospital admission, at the day of discharge and after discharge, following at least six weeks of clinical stability. Circulating endothelium-derived extracellular vesicles (eEVs) were quantified by flow cytometry and nucleosomes by ELISA. Results: Thrombin generation is increased and APC sensitivity is decreased independently of platelets in ADHF at admission compared to controls (p < 0.01). Thrombin generation was also increased in CHF but only in the presence of platelets. Plasma markers of endothelium activation (von Willebrand factor, factor VIII, procoagulant eEVs and circulating nucleosomes) and the ability of plasmas to induce neutrophil extracellular trap formation in control neutrophils are elevated in ADHF at admission compared to controls (p < 0.001). In-hospital prothrombotic changes in ADHF improved significantly at the post-discharge time-point. Circulating nucleosomes were positively correlated with APC sensitivity (p = 0.013) and annexin-V-positive eEVs (p = 0.004). Conclusions: This proof-of-concept study identified an endothelial-driven hypercoagulable phenotype at the acute phase of decompensated HF contrasting with the platelet-dependent prothrombotic state in CHF. These results highlighted a cross-talk between circulating eEVs and nucleosomes, procoagulant factors and impairment of the APC anticoagulant activity in ADHF.