Background The coronavirus disease 2019 (COVID-19) affected cancer care in Japan, but the detailed impact on cancer diagnosis and treatment is not well-understood. We aimed to assess the impact of COVID-19 on digestive cancer care in Osaka Prefecture, which has a population of 8.8 million. Methods We conducted a multi-center cohort study, using hospital-based cancer registry (HBCR) data linked to administrative data from 66 designated cancer care hospitals in Osaka. Records of patients diagnosed with cancer of the stomach, colorectum, esophagus, liver, gallbladder or pancreas were extracted from the HBCR data. Baseline characteristics, such as the number of diagnoses, routes to diagnosis and clinical stage, were compared between patients diagnosed in 2019 and those in 2020. We also compared treatment patterns such as the number of treatments (operations, endoscopic surgeries, chemotherapies, radiotherapies), pathological stage and time to treatment for each digestive cancer. Results In total, 62,609 eligible records were identified. The number of diagnoses decreased in 2020, ranging from -1.9% for pancreatic cancer to -12.7% for stomach cancer. Screen-detected cases decreased in stomach and colorectal cancer. The percentage of clinical stage III slightly increased across different cancers, although it was only significant for colorectal cancer. Among 52,741 records analyzed for treatment patterns, the relative decrease in radiotherapy was larger than for other treatments. The median time from diagnosis to operation was shortened by 2–5 days, which coincided with the decrease in operations. Conclusion The impact of COVID-19 on cancer care in 2020 was relatively mild compared with other countries but was apparent in Osaka. Further investigation is needed to determine the most affected populations.