Background: Studies assessing Spanish smoke-free laws have found a decrease in second-hand smoke exposure, but the impact of such laws on general smoking trends is not clear. This study proposes to analyse trends in the prevalence of smoking in Spain, including changes by educational level, following the implementation of smoke-free regulations (2005 and 2010). Methods: Seven editions of the Spanish Household Survey on Alcohol and Drugs from 1999 to 2011 were used to analyse the standardised prevalence of daily smokers, the proportion of ex-daily smokers, and the average cigarettes smoked daily in both sexes and by educational level, among the population aged 15–64. The annual percentage of change (APC), and Poisson and linear multiple regressions were used to identify differences in terms of years and educational levels. Results: The overall prevalence of Spanish daily smokers decreased from 33.5% in 1999 to 30.2% in 2011 (APC = −1.7% for men, APC = −1.0% for women). Differences between low and high educational levels in the prevalence of daily smokers and ex-daily smokers increased. For both sexes, the prevalence ratio (PR) of daily smokers was positive for the years before 2005 and negative afterwards. Conversely, for ex-daily smokers the PR in all years was lower than in 2005. The mean number of cigarettes decreased from 17.6 cig/day in 1999 to 14.2 in 2011 [APC= day 1.8 (95% confidence interval: day 2.2, day 1.3)]. Conclusion: Six years after the national smoke-free regulation was implemented, previously reported decreasing trends of smoking for both men and women persisted, while inequalities between educational levels increased in both sexes.