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The SARS-CoV-2 virus primarily infects salivary glands suggesting a change in the saliva metabolite profile; this shift may be used as a monitoring instrument during SARS-CoV-2 infection. The present study aims to determine the salivary metabolomic profile of patients with and post-SARS-CoV-19 infection. Patients were without (PCR-), with SARS-CoV-2 (PCR+), or post-SARS-CoV-2 infection. Unstimulated whole saliva was collected, and the 1 H spectra were acquired in a 500 MHz Bruker nuclear magnetic resonance spectrometer at 25 °C. They were subjected to multivariate analysis using principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA), as well as univariate analysis through t -tests (SPSS 20.0, IL, USA), with a significance level of p < 0.05. A distinction was found when comparing PCR- subjects to those with SARS-CoV-2 infection. When comparing the three groups, the PLS-DA cross-validation presented satisfactory accuracy (ACC = 0.69, R2 = 0.39, Q2 = 0.08). Seventeen metabolites were found in different proportions among the groups. The results suggested the downregulation of major amino acid levels, such as alanine, glutamine, histidine, leucine, lysine, phenylalanine, and proline in the PCR+ group compared to the PCR- ones. In addition, acetate, valerate, and capronic acid were higher in PCR- patients than in PCR+. Sucrose and butyrate were higher in post-SARS-CoV-2 infection compared to PCR-. In general, a reduction in amino acids was observed in subjects with and post-SARS-CoV-2 disease. The salivary metabolomic strategy NMR-based was able to differentiate between non-infected individuals and those with acute and post-SARS-CoV-19 infection.