Abstract Background Despite available information on trends in behavioral factors for Brazil and Argentina, little is known about the association of these trends with mortality. Understanding this association is important to avoid early deaths. Therefore, we aimed to evaluate temporal trends in behavioral risk and protective factors in Brazil and Argentina, and to assess their association with overall and cause-specific mortality rates. Methods Ecological study with data from two population surveys from Brazil and Argentina. Weighted prevalence of tobacco smoking, excessive alcohol consumption, fruit and vegetable consumption and physical activity for the 27 Brazilian state capitals and for the 23 Argentinean provinces were used as behavioral factors. Information on overall mortality as well as cardiovascular diseases and cancer mortality for the year 2015 was collected from national mortality banks of both countries. Estimated prevalence rates were used to describe trends in behavioral factors from 2006 to 2014 in Brazil, and from 2005 to 2013 in Argentina, while Pearson’s correlation and linear regression models were used to assess their association with overall and cause-specific mortality rates. Results Brazil presented improvements in behavioral risk and protective factors: sharp decrease in tobacco smoking prevalence (from 15 to 9%), increase in regular fruit and vegetable consumption (from 28 to 36%), and increase in physical activity (45 to 51%). In Argentina, results were more disappointing: small reduction in tobacco smoking (from 55 to 50%) and decrease in physical activity (from 55 to 45%). In both countries, excessive alcohol consumption remained stable, with increase only among women. The association between behavioral factors and mortality showed that in those Brazilian capitals with higher prevalence of regular consumption of fruits and vegetables, there were lower overall mortality rates. Stratification by gender revealed that significant results were only found among women. Conclusion Prevalence of regular consumption of fruits and vegetables increased in Brazilian capitals and was associated with lower overall mortality rate, suggesting a positive impact of Brazilian policies to improve dietary intake patterns on its population’s mortality. Approaches focusing on behavioral factors are especially needed in Argentina to reach similar results of those seen in Brazil.