Background: Saliva sampling is increasingly used for respiratory virus diagnostics in dentistry and oral medicine due to patient comfort and reduced exposure risk. How routine behaviors—mechanical oral hygiene, rinsing, and food intake—affect short-term SARS-CoV-2 detectability remains insufficiently characterized for clinical workflows. Methods: In this international two-center pilot study, twelve RT-PCR-confirmed COVID-19 patients provided paired mouth-rinse saliva samples and pharyngeal swabs at predefined time points. The study assessed (I) an intensified 3 min mechanical oral hygiene protocol (toothbrushing of teeth, gingiva, tongue, and palate, followed by toothpaste–saliva gargling); (II) repeated short mouth rinses; and (III) postprandial sampling. Viral RNA was quantified by RT-PCR; Ct-trajectories were analyzed intra-individually. Results: Cycle threshold (Ct) values from pharyngeal swabs remained relatively stable over time, whereas mouth-rinse samples exhibited notable fluctuations throughout the 24 h period. An average increase of 3 Ct units was observed three minutes after the final mouth rinse (T24+3). Meal ingestion was associated with increased Ct values, rising by 4–5 units for pharyngeal swabs and 3–11 units for mouth rinses immediately after eating. Conclusions: In clinical dental settings, saliva diagnostics are feasible but acutely modulated by common behaviors. Mechanical oral hygiene, brief rinsing, and food intake can transiently reduce detectable oral SARS-CoV-2 RNA, with potential implications for timing of sampling, chairside triage, and infection-control protocols. This pilot study provides initial evidence supporting the development of standardized pre-analytical instructions (e.g., fasting window, pre-rinse policy, and sampling timing relative to oral hygiene and meals) to enhance the reliability of saliva-based testing in dental care.