Determining emerging trends of clinical psychiatric diagnoses among patients infected with the SARS-CoV-2 virus is important to understand post-acute sequelae of SARS-CoV-2 infection or long COVID. However, published reports accounting for pre-COVID psychiatric diagnoses have usually relied on self-report rather than clinical diagnoses. Using electronic health records (EHRs) among 2,358,318 patients from the New York City (NYC) metropolitan region, this time series study examined changes in clinical psychiatric diagnoses between March 2020 and August 2021 with month as the unit of analysis. We compared trends in patients with and without recent pre-COVID clinical psychiatric diagnoses noted in the EHRs up to 3 years before the first COVID-19 test. Patients with recent clinical psychiatric diagnoses, as compared to those without, had more subsequent anxiety disorders, mood disorders, and psychosis throughout the study period. Substance use disorders were greater between March and August 2020 among patients without any recent clinical psychiatric diagnoses than those with. COVID-19 positive patients (both hospitalized and non-hospitalized) had greater post-COVID psychiatric diagnoses than COVID-19 negative patients. Among patients with recent clinical psychiatric diagnoses, psychiatric diagnoses have decreased since January 2021, regardless of COVID-19 infection/hospitalization. However, among patients without recent clinical psychiatric diagnoses, new anxiety disorders, mood disorders, and psychosis diagnoses increased between February and August 2021 among all patients (COVID-19 positive and negative). The greatest increases were anxiety disorders (378.7%) and mood disorders (269.0%) among COVID-19 positive non-hospitalized patients. New clinical psychosis diagnoses increased by 242.5% among COVID-19 negative patients. This study is the first to delineate the impact of COVID-19 on different clinical psychiatric diagnoses by pre-COVID psychiatric diagnoses and COVID-19 infections and hospitalizations across NYC, one of the hardest-hit US cities in the early pandemic. Our findings suggest the need for tailoring treatment and policies to meet the needs of individuals with pre-COVID psychiatric diagnoses.