Background: The COVID-19 pandemic has indirectly impacted health service provisions owing to surge and sustained pressures on the system. The effects of these pressures on the management of long-term or chronic conditions are not fully understood. Aim: To explore the effects of COVID-19 on the recorded incidence of 17 long-term conditions. Design and Setting: An observational retrospective population data linkage study on the population of Wales using primary and secondary care data within the Secure Anonymised Information Linkage (SAIL) Databank. Methods: We presented monthly rates of new diagnosis between 2000 and 2021 for each long-term condition. Incidence rates post-2020 were compared to expected rates predicted using time series modelling of pre-2020 trends. Proportion of annual incidence was presented by socio-demographic factors: age, sex, social deprivation, ethnicity, frailty and learning disability. Results: We included 5,476,012 diagnoses from 2,257,992 individuals. Incidence rates from 2020 to 2021 were lower than mean expected rates across all conditions. The largest relative deficit in incidence was in chronic obstructive pulmonary disease corresponding to 343 (95% CI: 230 to 456) undiagnosed patients per 100,000 population, followed by depression, type 2 diabetes, hypertension, anxiety disorders and asthma. A GP practice of 10,000 patients might have over 400 undiagnosed long-term conditions. No notable differences between socio-demographic profiles of post- and pre- 2020 incidences were observed. Conclusion: There is a potential backlog of undiagnosed patients across multiple long-term conditions. Resources are required to tackle anticipated workload as part of COVID-recovery, particularly in primary care.