Background: Periodontal disease is a chronic inflammation of periodontal tissues. Several systemic diseases are related to this condition. One of the strongest associations is that of periodontitis and type 2 diabetes mellitus (T2DM). On the contrary, the link with type 1 diabetes mellitus (T1DM) has not been extensively investigated. The objective of the present report is to evaluate and compare the effect of two domiciliary oral hygiene protocols on the periodontal clinical status as well as on the metabolic control in patients affected by T1DM. Methods: Sample size calculation required 20 patients per group, therefore 40 patients were equally and randomly assigned to the following home oral care protocols: a probiotic-based one (trial group) and a natural extracts-based one (control group). At the beginning of the study, after 3 and 6 months, the following periodontal indexes were collected: Probing Pocket Depth (PPD), Plaque Index (PI), Clinical Attachment Level (CAL), Bleeding on Probing (BoP), and Glycosylated Hemoglobin (HbA1c). Data underwent statistical analysis (significance threshold: p < 0.05). Results: In both groups, significant decreases in the periodontal clinical indexes were found at various time frames, whereas the levels of HbA1c significantly decreased only in the control group. Conclusions: Both the domiciliary treatments administered can significantly improve PPD, PI, CAL, and BOP parameters, whereas only the natural extracts-based gel seems to decrease HbA1c levels of T1DM patients.