The COVID-19 pandemic necessitated making timely managerial decisions when providing medical care to patients with tuberculosis (TB). The study aimed to develop a system for monitoring of TB combined with COVID-19 and estimate the prevalence of COVID-19 among TB patients, along with the efficacy of the measures applied. A registry of TB/COVID-19 patients was developed based on the Barclay-SV Medical Database Management System. It was used to perform comparative analysis of the information about 1837 patients with active TB forms and confirmed COVID-19 for two periods of the pandemic, 2020–2021 and 2022–2023, and against the data on all new TB cases and TB relapses registered in Moscow in 2020–2023: 7812 and 1243 individuals respectively, from the TB surveillance registries, excluding those identified posthumously. The socio-demographic structure of patients with TB/COVID-19 co-infection identified in 2020–2023 did not change and corresponded to that of TB patients. In the second period analyzed, mild COVID-19 cases were registered more often (60.9% vs. 41.6%; p < 0.01), the share of moderate COVID-19 cases decreased from 48.2% to 20.6% (p < 0.01), and the share of severe cases decreased from 6.4% to 4.9% (p = 0.19). In 2022–2023, the share of individuals with COVID lung damage decreased from 45.1% to 17.6%, while the number of cases of COVID upper respiratory tract lesion increased from 47.1% to 64.5% (p < 0.05). The fact of having HIV infection, CAD and hypertension, kidney and genitourinary diseases increased the chance of developing COVID-19 by TB patients 1.5–2-fold, and disseminated pulmonary tuberculosis, caseous pneumonia, lung tissue destruction and bacterial excretion increased it 1.4–1.6-fold. The registry made it possible to control routing of TB/COVID-19 patients, as well as treatment outcomes: the total share of individuals cured reached 90.1%.