[4] San Ignacio has been closely linked to Deportivo Alavés at various times; it was the formative club of Spain international forward Ernesto Valverde.

In 2002, San Ignacio achieved promotion to the Tercera División RFEF again, but once again they weren't able to hold on for more than a season, being relegated at the end of the 2002-03 campaign.

[citation needed] 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.

[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.

[3] For the 2011–12 season, the collegiate club launched a subsidiary in the First Regional of Álava (7th tier of Spanish football) to release the youth players who finished that stage.