Abstract Background During the COVID-19 pandemic, the incidence of chronic disease had drastically been reduced due to health care interruptions. The aim of this study is to analyse cancer diagnosis during the last 2 years of the COVID-19 pandemic. Methods Time-series study of cancer diagnoses recorded in primary care settings, using data from the primary care electronic health records from January 2014 to December 2021. We obtained the expected monthly rate per 100,000 inhabitants using a time regression adjusted by trend and seasonality. We additionally compared rates of cancer diagnoses in 2019 with those of 2020 and 2021 using the t-test. We performed the analysis globally, by sex and by type of cancer. Results In 2020, the rate of cancer diagnoses had reduced by −21% compared to 2019 (P < 0.05). Greater reductions were observed during the lockdown in early 2020 (>40%) and with some types of cancers, especially prostate and skin cancers (−29.6% and −26.9%, respectively, P < 0.05). Lung cancers presented statistically non-significant reductions in both years. Cancer diagnosis returned to expected around March 2021, and the rate in 2021 was similar to that of 2019 (overall difference of 0.21%, P = 0.967). However, an 11% reduction was still found when comparing the pandemic months of 2020–2021 with pre-pandemic months. Conclusions Although primary care cancer diagnoses in 2021 have returned to pre-pandemic levels, missing diagnoses during the last 2 years have not been fully recovered.