The impact of COVID-19 on systemic immunity in the general population has been well characterized, however the short-term effects of COVID-19 infection on innate salivary immunity in elite-level athletes are unknown. Therefore, this study aimed to determine whether elite college football athletes had altered salivary immunity following the CDC-recommended isolation post-SARS-CoV-2 infection. Salivary samples were obtained from fourteen elite football players who tested positive for SARS-CoV-2 (n = 14), immediately after CDC-recommended isolation (average days = 14 ± 2 days) and fifteen controls who remained uninfected with SARS-CoV-2. Biomarkers of innate salivary immunity (sIgA and alpha-amylase), antimicrobial proteins (AMPs, i.e., HNP1-3, lactoferrin, LL-37) and lung inflammation (SPA, SPLI, and Neutrophil Elastase-alpha-1-antitrypsin complex) were measured. Independent student t-tests were used to determine changes in biomarkers between groups. Although all AMP levels were within normal range, Human Neutrophil Defensin 1-3 concentrations and secretion rates were higher in SARS-CoV-2+ compared to SARS-CoV-2-. This suggests that the CDC-recommended isolation period is sufficient to ensure that athletes' salivary immunity is not compromised upon return to sports, and athletes post-COVID-19 infection do not appear to be at greater risk for secondary infection than those with no history of COVID-19.