In 2003, San Ignacio (who had previously been associated with Real Sociedad) agreed a four-year partnership with Deportivo Alavés to host their second reserve team in Tercera División.[5] The affiliate became known as Alavés C-San Ignacio,[6] maintaining the Alavés name but playing in San Ignacio colours and usually hosting fixtures at their home ground.[5] When this entity was relegated in 2004–05, the Alavés link was discontinued.
San Ignacio continued operating independently and returned to the Tercera level twice (on each occasion their opponents included the other reserve side of Alavés,[5] with both teams being relegated in 2008–09). The club remains a partner club of Alavés.[7][8] They were promoted again in 2017–18,[9] with Alavés offering use of their Ibaia facilities for matches at that level due to the Federation being concerned with the condition of the playing surface at Adurtzabal.[10] Further progression to the Segunda División B (never achieved by the club) was a possibility in 2018–19 until defeat in the playoffs.[11]
^"Clubes Convenidos" [Partner Clubs] (in Spanish). Deportivo Alavés. 1 August 2017. Archived from the original on 8 March 2018. Retrieved 8 March 2018.