Born in San Sebastián, Gipuzkoa, Prieto was a graduate of the youth system at his hometown club Real Sociedad, having joined from school aged 16 and spent time on loan with local amateurs :es:Club Deportivo Hernani|CD Hernani. He made his senior debut in 2002 with the reserves, helping them to achieve promotion to Segunda División B in his first season. After starting the next campaign with the B-side, Prieto made his made his first-team debut on 8 October 2003, playing the full 90 minutes in a 2–1 away win against Real Oviedo for the Copa del Rey. His La Liga bow took place 18 days later, coming off the bench in a 1–0 home victory over Navarrese neighbours CA Osasuna; he would go on to collect a further eight substitute appearances – seven of them late in the game – during that season. However, on 23 May of the following year, with the league's outcome already decided, he profited from his second start to score twice against Real Madrid in a 4–1 away success, one of the goals coming from the penalty spot. Subsequently, Prieto was definitely promoted to the first squad and, in 2005–06, participated in all 38 games and netted nine times, six of them being penalties. In the following campaign he was also ever-present, but the Basques dropped down to Segunda División. Prieto played in 35 matches in 2009–10, totalling exactly 3,000 minutes and contributing with seven goals as Real Sociedad returned to the top level after three years. In the first game of the following season, at home against Villarreal CF, he scored the game's only goal after a backheel pass from newly signed Joseba Llorente. On 6 January 2013, Prieto netted the first hat-trick of his professional career, albeit in a 3–4 loss at Real Madrid: he scored once through a penalty and twice after one-on-one situations against Iker Casillas. He added a brace on 22 February 2015 in another seven-goal thriller, but now in a 4–3 home win over Sevilla FC; in the interim, he made seven appearances for the Txuriurdin in the 2013–14 edition of the UEFA Champions League. On 25 August 2017, Prieto played his 500th game for the Real Sociedad first team a few days prior to his 34th birthday, and marked the occasion with a goal in a 3–0 defeat of Villarreal at the Anoeta Stadium. He also received an ovation from supporters in the tenth minute, his shirt number, and a few weeks later he broke the club record for most league appearances. In April 2018, Prieto confirmed he would be retiring at the end of the season. To honour his contributions, Real Sociedad arranged for the club crest to be replaced with his portrait on the players' shirts for the final match of the campaign against CD Leganés.
