Puerto Rico (PR) has faced environmental and public health challenges that could have significantly affected access to cancer screening. Using administrative data from claims from the Medicaid population in PR, this study evaluated trends in colorectal and breast cancer detection from 2016 to 2021, the impact of disasters on detection, and the absolute deficit in detection due to the pandemic. The monthly claim rates were analyzed using Poisson regression. Significant reductions were seen in the use of screening for breast and colorectal cancer. The colorectal cancer detection rate in 2017 was 77% lower one month after hurricanes Irma and Maria [Adjusted RR: 0.23; 95% CI: 0.20, 0.25] compared to the same period in 2016. Breast cancer detection fell 50% in November 2017 compared to November 2016 [Adjusted RR: 0.50; 95% CI: 0.47, 0.54]. Prospectively, only a recovery has been observed in use for the detection of breast cancer. The results revealed that the use of cancer screening decreased substantially after environmental disasters and the pandemic. These findings have potential serious long-term implications for cancer health disparities and mortality in PR.