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 fired in mid-October after only eight games (four draws and four losses), and the former stayed on as second in command to
Carlos Ríos. Merino was named manager of
Xerez CD on 14 June 2011. He was sacked on 4 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 relieved of his duties the following 20 May as the team was still in
the relegation zone. On 18 October 2017, Merino replaced the dismissed
Luis Carrión at the helm of
Córdoba CF, still in the second division. He was fired on 7 December after winning none and drawing three of his seven fixtures. Merino returned to management on 29 April 2019, taking over from
Pedro Munitis at
UCAM Murcia CF and tasked with taking the team to
play-offs of
Segunda División B in their final three games. ==Managerial statistics==