COVID-19 has disrupted the treatment of non-communicable diseases (NCDs). This study conducted a multimorbidity analysis and evaluated hospital admissions and death rates among diabetic patients before and after the implementation of lockdown due to the COVID-19 pandemic in Peru. Data from the Ministry of Health (MINSA) of Peru from January 2017 to December 2020 was used. Hospital death, discharge and the percentage of death/hospital admissions were defined as outcomes of interest. We performed an interrupted time series analysis to assess the aggregate change in the outcomes of interest before and after mandatory lockdown in response to the COVID-19 pandemic in Peru (n = 65,935). Additionally, a network analysis was performed to evaluate the frequency of occurrence of hospital admissions before and after the mandatory lockdown according to demographic characteristics. The average monthly hospital admissions among diabetic patients in Peru decreased by 29% after the implementation of the lockdown. The largest reduction was observed in women (−41%) and for patients 60 years or older (−35%). Furthermore, there was a 92% increase in the average number of monthly deaths. The largest percentage change occurred in men (+113%) and in the group of 40–59 years (+144%). After the implementation of lockdown in Peru, hospital admissions among diabetic patients significantly decreased while in-hospital mortality slightly increased. Our findings shed light on the limitations of the Peruvian health system and the importance of ensuring continued care of NCDs as part of the response strategy during times of crisis.