(1) Background: This study aimed to assess the periodontitis burden in systemic sclerosis patients and the possible association between them, and the degree to which some potential risk factors and two potential diagnostic biomarkers may account for this association. (2) Methods: This cross-sectional study included a test group (systemic sclerosis patients) and a control group (non-systemic sclerosis patients). Both groups benefited from medical, periodontal examination and saliva sampling to determine the salivary flow rate and two inflammatory biomarkers (calprotectin, psoriasin). A systemic sclerosis severity scale was established. (3) Results: In the studied groups, comparable periodontitis rates of 88.68% and 85.85%, respectively, were identified. There were no significant differences in the severity of periodontitis among different systemic sclerosis severity, or in the positivity for anti-centromere and anti-SCL70 antibodies. Musculoskeletal lesions were significantly more common in stage III/IV periodontitis (n = 33, 86.84%) than in those in stage I/II (n = 1, 100%, and n = 3, 37.5%, respectively) (p = 0.007). Comparable levels of the inflammatory mediators were displayed by the two groups. There were no significant differences in calprotectin and psoriasin levels between diffuse and limited forms of systemic sclerosis. (4) Conclusions: Within the limitations of the current study, no associations between systemic sclerosis and periodontitis, or between their risk factors, could be proven.