The Great Recession hit Spain deteriorating the living conditions of many Spanish people, increasing the prevalence of several chronic health issues, including obesity, and affecting health inequalities. We analyse the impact of this economic crisis on body mass index (BMI) disparities in Spain, from two perspectives: the socioeconomic and the territorial, through the application of an intersectional multilevel analysis of individual heterogeneity and discriminatory accuracy. We use data from the Spanish National Health Surveys of 2006/2007, 2011/2012 and 2016/2017 to build multilevel linear regression models and estimate BMI averages and components of variance. We find a greater increase in the overall average BMI and a widening of the socioeconomic disparities during the hardest years of the crisis. However, these differences decreased when the economic situation in the country began to improve. Both socioeconomic and geographical information contribute to mapping the distribution of BMI in the population. However, according to the ICC values, considering the regional perspective provides a better understanding of the distribution of the BMI, during the period of economic crisis, in the Spanish population. Therefore, regional policies can play an important role in counteracting obesity in times of crisis.