Born in La Línea de la Concepción, Province of Cádiz, Merino joined Real Betis's first team in 1990, becoming their captain in later years. Out of his twelve years at the club eight were in La Liga, and he appeared in 203 games in that division, scoring two goals and surpassing overall 300 appearances; in the 1996–97 season, he contributed with 36 matches to help to a fourth-place finish. In 2002–03, staying in Andalusia, Merino joined Recreativo de Huelva. In his first season the side was relegated, regaining top flight status in 2006. After featuring in 23 games in the 2006–07 campaign he retired from football, with more than 500 official matches played – both major levels combined.
Coaching career
Immediately after retiring, Merino rejoined Betis as director of football. He was named assistant coach in 2009, going on to work with two different managers. In the 2010–11 season, Merino cut ties with Betis and returned to Recre as assistant to Pablo Alfaro – a former Sevilla FC defender – with the club in the Segunda División. The latter was sacked in mid-October after only eight games, and the former stayed on as second in command to Carlos Ríos. On 14 June 2011, Merino was named manager of Xerez CD. He was sacked on 5 December, due to poor results. On 25 June 2014, after nearly three years without a club, Merino was appointed at the helm of Betis B. On 25 November, after Julio Velázquez's dismissal from the first team, he was named interim manager; he remained in charge for four league matches, achieving as many wins before being replaced by Pepe Mel and returning to his previous duties. On 11 January 2016, Merino was again appointed caretaker manager at Betis, following Mel's sacking. On 3 February, he was chosen to remain in the position until the end of the season. On 25 May 2016, after the arrival of new boss Gus Poyet, Merino left Betis. On 28 December, he took over at second tier club Gimnàstic de Tarragona in the place of Vicente Moreno, but was himself sacked the following 20 May as the team was still in the relegation zone. On 18 October 2017, Merino replaced sacked Luis Carrión at the helm of Córdoba CF, still in the second division. He was sacked on 7 December after winning none and drawing three of his seven fixtures. Merino returned to management on 29 April 2019, replacing Pedro Munitis at UCAM Murcia CF and tasked with taking the team to the Segunda Bplay-offs in their final three games.