It is becoming increasingly clear that individuals recovered from acute coronavirus disease 2019 (COVID-19) can develop into long-term sequelae termed ‘long coronavirus disease’ or ‘post-acute sequile SARS-CoV-2 infection’ (PACS). While most common manifestations of PACS are presented as systemic and long term, the early molecular mechanisms involved in the development of the sequelae remain elusive. To further understand immune responses globally after exposure to the virus, we surveyed plasma and saliva samples from COVID-19 and control - pre-pandemic- individuals. Initial serology investigation verified robust IgA and IgG responses with neutralizing activity to the SARS-CoV-2 and showed detection and positive correlations between paired plasma and saliva. To monitor immune pathways, we assayed our biofluids via shotgun proteomics. A dysbiosis in the proteomic profiles specially in persistent inflammatory patterns was detected in COVID-19 cases, revealing dysfunction of neutrophil-fibrinogen axis, relevant to immune and clotting functions. Overall our results reveal early dysbiotic immune markers, even when protective antibodies are found, demonstrating that serology is not sufficient to understand the health status. Additionally, we present saliva as a viable means to monitor serology, chronic inflammation and immune functions. Further delineation of the disease pathogenesis may provide biomarker and therapeutic targets to patients at risk to develop Post acute sequelae SARS-CoV-2 infection (PASC).