Introduction: Systemic sclerosis (SSc) is characterized by fibrosis and vascular abnormalities of skin and internal organs. Cardiac involvement includes coronary artery disease (CAD), pulmonary arterial hypertension (PAH) related right ventricular changes and microvascular disease (MVD). Aims: To characterize the distribution of cardiac alterations and to investigate the mechanisms of the microvascular impairment of SSc patients. Methods: Based on non-invasive investigations, patients were selected for right heart catheterization and intracoronary pressure-wire supplemented coronary angiography. Results: 17 SSc patients (selected from 120 cases) and 17 controls were enrolled. In the "suspected PAH" and the "suspected CAD" groups, PAH was found in 12/20 and 2/10 cases, and coronary artery stenosis in 9/20 and 6/10 cases, respectively. Patients with decreased coronary flow reserve (CFR) had accelerated flow velocity (p < 0.05), but myocardial resistance index (IMR) in hyperemia did not differ from patients with normal CFR or from the controls (p = 0.292 and p = 0.308). The coronary flow velocity of SSc patients correlated to the IMR at baseline (r = 0.56, p = 0.019). Conclusions: PAH, CAD and MVD show an overlap in symptomatic SSc. The maintained vasodilatation response indicates the paucity of irreversible functional damage of the coronary arterioles. The reduced CFR, the decreased basal IMR and higher velocity pinpoint to possible compensatory vasodilatory mechanisms.