Llera was born in Castilleja de la Cuesta, Province of Seville. After unsuccessfully emerging through local Recreativo de Huelva's youth ranks, he represented several modest clubs until 2005–06, when he contributed with 27 games to Gimnàstic de Tarragona's return to La Liga after a 56-year absence; midway through the following season, however, he was released from contract after appearing in 12 matches for the Catalans and scoring in defeats against Real Sociedad and Getafe CF, as Nàstic were immediately relegated. In 2007–08 Llera continued in Segunda División, but also failed to impress at Hércules CF, playing only 11 games out of a possible 42.
After a successful season, with a third-place finish straight out of Football League Two, albeit without eventual promotion, Llera signed for Charlton Athletic on 2 July 2009, after turning down a new contract offer – he became the first Spanish footballer to play for the club. Llera quickly established himself as a fans' favourite after just four matches, scoring on his debut against Wycombe Wanderers but also picking up a head injury which led him to wear a helmet for the next fixtures, similar to that of Chelsea's Petr Čech; he scored his first goal for the Addicks on 22 August 2009, in a 2–0 home win against Walsall.
After leaving Charlton at the end of the 2010–11 season, Llera spent some time training with Blackpool and joined them on trial, making his debut against Rangers on 19 July 2011. On 2 August, he scored from a free kick against Lancaster City in a 1–3 defeat, and, two days later, he signed a one-year contract with the option of a further year.
On 7 September 2011, Llera transferred to Brentford on a three-month loan deal. On 22 November he moved to Sheffield Wednesday, in a loan agreement lasting until January 2012. On 10 January 2012, Llera was signed on a permanent deal by Wednesday, having been released by Blackpool. On 11 February, in a game against Exeter City, he suffered a head injury in an eventual 1–2 away loss, going on to miss approximately one month of action.
Scunthorpe
After impressing on trial, on 21 July 2014 Llera was offered a contract by Oldham Athletic, which was later withdrawn. He eventually moved to League One's Scunthorpe United late in the month, agreeing to a one-year deal also after a trial period. Llera made his competitive debut on 9 August 2014, in a 1–3 defeat at Swindon Town. His first appearance at Glanford Park took place the following weekend, and he scored a 39th minute own goal in 0–4 loss to Preston North End. Llera netted his first and only goal for the Iron on 13 December 2014, contributing to a 2–1 home win over Crewe Alexandra. On 5 May of the following year, it was announced he would not be offered a new contract and was free to leave the club.
In July 2014, Llera began coaching the under-14 squad of Sheffield Wednesday. In summer 2015, he started working as a first-team scout. In January 2016, Llera launched his own academy, Miguel Llera International Football Academy, occasionally sending young players for trials at Wednesday. In August 2017, he was appointed Professional Development Phase coach at Chesterfield. On 11 January 2019, Llera left the Proact Stadium by mutual consent.
Starting in July 2015 and with the duration of one year, Llera was part of the staff at Sheffield FC, acting as assistant manager as well as being responsible for subjects concerning the academy. In September 2015, he became the club's scholarship football coach and also second and third team manager at Sheffield Hallam University; in addition, he held the same position at Meadowhead School Academy Trust. Llera left all of these roles in September 2016.
