Background: The aim of this study was to analyze the trend in socioeconomic inequalities in mortality in small areas due to several specific causes before (2001–2004, 2005–2008) and during (2009–2012) the economic crisis in seven Spanish cities. Methods: This ecological study of trends, with census tracts as the areas of analysis, was based on three periods. Several causes of death were studied. A socioeconomic deprivation index was calculated for each census tract. For each small area, we estimated standardized mortality ratios, and controlled for their variability using Bayesian models (sSMR). We also estimated the relative risk of mortality according to deprivation in the different cities, periods, and sexes. Results: In general, a similar geographical pattern was found for the socioeconomic deprivation index and sSMR. For men, there was an association in all cities between the deprivation index and all-cause mortality that remained stable over the three periods. For women, there was an association in Barcelona, Granada, and Sevilla between the deprivation index and all-cause mortality in the third period. Patterns by causes of death were more heterogeneous. Conclusions: After the start of the financial crisis, socioeconomic inequalities in total mortality in small areas of Spanish cities remained stable in most cities, although several causes of death showed a different pattern.