BackgroundNursing homes (NHs) have been particularly affected by COVID-19. The aim of this study is to estimate the burden of COVID-19 and to investigate factors associated with mortality during the first epidemic wave in a large French NHs network.MethodsAn observational cross-sectional study was conducted in September-October 2020. 290 NHs were asked to complete an online questionnaire covering the first epidemic wave on facilities and resident characteristics, number of suspected/confirmed COVID-19 deaths, and preventive/control measures taken at the facility level. Data were crosschecked using routinely collected administrative data on the facilities. The statistical unit of the study was the NH. Overall COVID-19 mortality rate was estimated. Factors associated with COVID-19 mortality were investigated using a multivariable multinomial logistic regression. The outcome was classified in 3 categories: “no COVID-19 death in a given NH”, occurrence of an “episode of concern” (at least 10% of the residents died from COVID-19), occurrence of a “moderate episode” (deaths of COVID-19, less than 10% of the residents).ResultsOf the 192 (66%) participating NHs, 28 (15%) were classified as having an “episode of concern”. In the multinomial logistic regression, moderate epidemic magnitude in the NHs county (adjusted OR = 9.3; 95%CI=[2.6–33.3]), high number of healthcare and housekeeping staff (aOR = 3.7 [1.2–11.4]) and presence of an Alzheimer’s unit (aOR = 0.2 [0.07–0.7]) were significantly associated with an “episode of concern”.ConclusionsWe found a significant association between the occurrence of an “episode of concern” in a NH and some of its organizational characteristics and the epidemic magnitude in the area. These results can be used to improve the epidemic preparedness of NHs, particularly regarding the organization of NHs in small units with dedicated staff.Brief summaryFactors associated with COVID-19 mortality and preventive measures taken in nursing homes in France during the first epidemic wave.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12877-023-04078-8.