Background Controversies about the 2009 H1N1 pandemic influenza vaccination might have impacted the motivational processes that underlie individual immunization against seasonal influenza. The purpose of this article is to investigate correlates of vaccine uptake during and after the pandemic. Methods Data from the 1174 subjects of the CoPanFlu France cohort aged 15 and over were used. We used logistic regression models to identify social and behavioral predictors of getting vaccinated against seasonal influenza in 2009–2010 and in 2010–2011 and against H1N1 influenza in 2009–2010. Results This study points out that correlates of vaccination behaviors varied according to the vaccine. Respondents under 65 years who adopted the seasonal influenza vaccine were, as usual, more likely to belong to a target group and have a lower education, contrary to subjects who chose the pandemic vaccine. Exceptionally during the pandemic, a higher socioeconomic status also led to adoption of either vaccine. Motivational processes differed by vaccine. Uptaking the “new” pandemic vaccine was the result of a deliberative decision-making process, influenced by cognitive factors related to the pandemic context (such as perceived severity of the H1N1 flu strain and trust in public health authorities). In contrast, respondents got the seasonal flu vaccine without relying on explicit justifications, but instead through habit of performing this behavior in the past. Conclusions Target groups for seasonal influenza but not those for pandemic influenza were more likely to adopt the pandemic vaccine, which is a cause for great concern. This may be due to large extent to the automatic and habitual nature of influenza vaccination decisions. Public health authorities, should pay more attention to situational than informational cues to facilitate vaccine uptake among priority groups, especially in case of mild pandemic influenza.