In December 2009, Etxeberria made himself available for the vacant managerial position atDorchester Town in theConference South, the sixth tier of theEnglish football league system.[5] He was made a consultant and first-team coach while the search for a permanent manager was delayed by legal issues between the club and its former chairman.[6] In March 2010, caretaker managerAshley Vickers was given the job permanently and Etxeberria returned to Spain to becomedirector of football atDeportivo Alavés in theSegunda División B.[7] He resigned from the club fromVitoria-Gasteiz in May 2011, with weeks of his contract remaining.[8]
Etxeberria was hired as manager and director atUD Salamanca in June 2012, with the third-tier club being in serious economic problems.[9] He was dismissed from his coaching position the following 4 March and replaced withB-team manager José María Hernández, as the club was dissolved at the end of the season.[10]UDS was succeeded by the corporately relatedSalamanca CF UDS, and the fan-drivenUnionistas de Salamanca CF; in 2019 Etxeberria said that he had spoken toSalamanca's mayor in a failed attempt to ensure there was only one successor.[11]
In August 2013, Etxeberria turned down an approach fromCaudal Deportivo in Spain's third tier and a youth team from his hometown in order to joinAtlético Clube de Portugal in the neighbouring country'sSegunda Liga.[12] Having taken 12 points from 14 games, and with theLisbon-based club in 19th place, he left on 9 November.[13]
After three years as director ofCD Hernani in his nativeGipuzkoa, Etxeberria headed abroad again in June 2017, on an 18-month deal atSydney Olympic FC of the second-tierNational Premier Leagues NSW.[2] He was sacked on 2 March 2018 as the first dismissal of the season, and replaced byAbbas Saad.[14] In February 2020, he and Chris Taylor ofSouth Melbourne FC were awardedAU$80,000 in compensation each by aFIFA tribunal, which ruled that they were wrongfully dismissed.[15]
In June 2018, Etxeberria returned to Salamanca as director of Unionistas.[16] He left in November 2019, with the club second from bottom.[17] The following January, he was hired on an 18-month deal atReal Unión in his home province.[18] On 25 February 2020, the club fromIrun sacked Alberto Iturralde and put Etxeberria in caretaker charge as manager.[19] In June 2021, with the club promoted to the newPrimera Federación and under ownership ofUnai Emery's family, he signed a one-year contract extension.[20] He left at its end.[21]
Etxeberria was hired in another directorial role atCF Rayo Majadahonda in June 2022.[22] He lasted only weeks before being replaced byNéstor Susaeta.[23] In January 2023, he returned to the city ofZaragoza after nearly 15 years away, joiningCD Ebro in the same position.[24]