After two seasons, Edu was officially signed for €2,000,000 in 2006. On the final day of 2006–07 he scored twice in the final ten minutes in a 2–0 win at Racing de Santander, which proved instrumental in avoiding relegation to the second division. In the following season, as Betis again battled relegation, he finished as the club's top scorer at 12; two of those came on 29 March 2008 as he netted the first and the last for his team in a 3–2 home win against FC Barcelona, who led 2–0 at half-time.