Abstract Background The main goal of this work is to estimate the actual number of cases of COVID-19 in Spain in the period 31 January 2020 to 01 June 2020 by Autonomous Communities. Based on these estimates, this work allows us to accurately re-estimate the lethality of the disease in Spain, taking into account unreported cases. Methods A hierarchical Bayesian model recently proposed in the literature has been adapted to model the actual number of COVID-19 cases in Spain. Results The results of this work show that the real load of COVID-19 in Spain in the period considered is well above the data registered by the public health system. Specifically, the model estimates show that, cumulatively until 1 June 2020, there were 2 425 930 cases of COVID-19 in Spain with characteristics similar to those reported (95% credibility interval: 2 148 261–2 813 864), from which were actually registered only 518 664. Conclusions Considering the results obtained from the second wave of the Spanish seroprevalence study, which estimates 2 350 324 cases of COVID-19 produced in Spain, in the period of time considered, it can be seen that the estimates provided by the model are quite good. This work clearly shows the key importance of having good quality data to optimize decision-making in the critical context of dealing with a pandemic.