El-Abd joined Brighton's youth department when he was ten and was granted a scholarship there at 16. He signed his first professional contract of two-and-a-half years with Brighton & Hove Albion at the age of 19. He made his full league début for the club in the 2–1 win at Notts County in November 2003. He has since been a regular in the first team squad and can play either in defence at right-back or centre-half, or in a more defensive midfield type role. During the game at Huddersfield Town on 18 March 2008, El-Abd was stretchered off with medial collateral ligament damage and ruled out for the remainder of the season. In June 2008, El-Abd signed a new two-year deal with Brighton. He won the Brighton & Hove Albion Player of the Season award for their League One winning 2010–11 campaign. El-Abd hit the milestone of 250 league appearances for Brighton and Hove Albion on 7 March 2012, named Man of the Match for that game, a 2–2 draw with Cardiff City. El-Abd made his 300th and final league appearance for Brighton coming on as a 90th-minute substitute against Birmingham City on 11 January 2014.
On 16 January 2014, El-Abd transferred to League One club Bristol City for an undisclosed fee. Rarely used at Bristol City, he spent time out on loan at Bury, Swindon Town, and Gillingham.
After his contract at Bristol City expired, he moved to League One club Shrewsbury Town on a free transfer in July 2016, signing a two-year contract, where he immediately became captain in place of the departed Nathaniel Knight-Percival. He scored his first goal for the club in a 2–1 home victory against Chesterfield on 20 August, but was sent off in a 2–1 defeat at former club Bury three weeks later. After the departure of Shrewsbury manager Micky Mellon, El Abd scored a "30 yard half-volley" in a 1–1 draw away at Southend United on 29 October, to hand new boss Paul Hurst a point in his first match in charge. El-Abd left the club at the end of June 2017 after his contract was cancelled by mutual consent.
On 3 July 2017, El-Abd signed a two-year contract with League Two side Wycombe Wanderers. In May 2018 he extended his contract for a further year, to the end of the 2019–20 season. El-Abd left Wycombe on 2 September 2019 by mutual consent.
Stevenage
He signed for Stevenage on 6 September 2019, but was released by the Hertfordshire side at the end of the 2019–20 season having made just 4 appearances in all competitions.
