Background: The post-acute impact of SARS-CoV-2 infections on chronic conditions remains poorly understood, particularly in general populations. Objectives: Our primary aim was to assess the association between SARS-CoV-2 infections and new diagnoses of chronic conditions. Our two secondary aims were to explore geographic variations in this association and to assess the association between SARS-CoV-2 infections and the exacerbation of pre-existing conditions. Methods: This longitudinal study used data from 8086 participants of the Specchio-COVID-19 cohort in the canton of Geneva, Switzerland (2021–2023). Mixed-effects logistic regressions and geographically weighted regressions adjusted for sociodemographic, socioeconomic, and healthcare access covariates were used to analyze self-reported SARS-CoV-2 infections, new diagnoses of chronic conditions, and the exacerbation of pre-existing ones. Results: Participants reporting a SARS-CoV-2 infection were more likely to be diagnosed with a new chronic condition compared to those who did not report an infection (adjusted odds ratio [aOR] = 2.15, 95% CI 1.43–3.23, adjusted p-value = 0.002). Notable geographic variations were identified in the association between SARS-CoV-2 infections and new diagnoses. While a positive association was initially observed between SARS-CoV-2 infections and exacerbation of pre-existing chronic conditions, this association did not remain significant after adjusting p-values for multiple comparisons. Conclusions: These findings contribute to understanding COVID-19’s post-acute impact on chronic conditions, highlighting the need for targeted health management approaches and calling for tailored public health strategies to address the pandemic’s long-term effects.