The objective was to identify the chronic impact of SARS-CoV-2 virus infection in new diagnostics, pharmacological prescriptions, and use of healthcare resources in patients after acute infection in a case-control study. Methods: Case-control study with observation of new diagnostics codified in the Electronic Health Recordings, with a total population of 604,000 subjects. Cases included patients diagnosed with acute infection. Matched controls in the absence of infection using a Propensity Score were also included. Observational period was 6 months. New diagnostic (CIE10), prescriptions and visits to Health Care Resources were identified. Results: 38,167 patients with a previous COVID infection and the same number of controls were analyzed. Population included < 18 years old, 7586 (mean age 10.2 years, girls 49%), and 30,581 adults (mean age 46.6 years, females 53%). In adults, 25% presented new diagnoses, while the prevalence was 16% in youth. A total of 40 new diagnostics were identified. The most frequent were diagnostics in the neuropsychiatric sphere, with older age, female, and previous admission in the Critical Care Unit being the factors related in adults, while in youth higher age was also a factor. Prescription of psychoanaleptic, psycholeptic and muscle relaxants had increased. An increment of around 20% in visits to Primary Care Physicians, Specialists and Emergency Departments was registered. Conclusion: Compared with a control group, an increment in the number of new diagnostics, new prescriptions and higher use of Health Care resources were observed. Many of the new diagnoses also occur in non-infected subjects, supporting the complex origin of so-called Long-COVID.