Allen made a first start on 14 August 2007 in a 2–0 home win over Walsall in the first round of the League Cup. He was named man of the match for his performance, which included assisting in the first goal by providing a left-footed chipped cross to Paul Anderson. Two days later, Martínez awarded Allen his first professional contract, to keep him at Swansea until 2010. Allen started in the next round of the tournament at home to Reading and again received the man of the match award, despite a 1–0 loss. He made 14 appearances over the campaign, six in the Swans’ victorious capture of the League One title.

Soon after receiving his first professional contract for Swansea City in August 2007, Allen was called up for the Wales under-21 team in a friendly match away to Sweden. He scored the winning goal in a 4–3 victory.

The following season, Swansea’s first in the Championship, Allen struggled to get into the first team due to competition from midfielders Darren Pratley, Ferrie Bodde, Owain Tudur Jones, Jordi Gómez and Leon Britton. On 7 October 2008, Allen joined Conference Premier club Wrexham on a one-month loan and scored a goal from 25 yards on his debut for the North Wales team the same day, in a 3–1 win over York City at the Racecourse Ground. His loan was curtailed after only one more match, when he damaged ankle ligaments and was sidelined for a month. Allen returned from the injury in December, entering the Swansea squad at home to Barnsley after regular midfielder Ferrie Bodde had been ruled out for the remainder of the season due to injury. With Swansea 2–0 down and playing poorly, manager Martínez was prompted to bring Allen on from the substitutes’ bench. The club went on to earn a late 2–2 draw and despite only playing 25 minutes, Allen once more received the man of the match award. On 5 April 2009, Allen came on as a 68th-minute substitute for Mark Gower, and 20 minutes later scored his first goal for Swansea in a South Wales derby 2–2 draw away at Cardiff City. At the end of the season, he signed a new three-year contract lasting until 2012.

In May 2009, Allen made his debut for the senior Wales team as an 80th-minute substitute for Jack Collison during a friendly against Estonia. Wales, who won 1–0 in Llanelli, were fielding their youngest team ever, with an average age of 21. He made his first start for Wales in a 2–0 UEFA Euro 2012 qualifying Group G match against Switzerland at his club’s Liberty Stadium in October 2011. He was awarded the prize for the Wales’ Player of the Year for 2012 in October of that year.

After frequently being injured in the 2009–10 season, Allen returned to regular first-team football at the start of the 2010–11 season. A string of impressive performances prompted manager Brendan Rodgers to play Allen in the South Wales derby in November 2010, with Allen receiving the man of the match award in the 1–0 win. He played 40 league matches and scored twice over the Championship campaign, and featured for the full 90 minutes as Swansea won promotion with a 4–2 victory over Reading in the play-off final at Wembley Stadium. However, he scored an own goal in that match.

A few days prior to the beginning of the 2011–12 Premier League, Allen signed a new four-year contract with Swansea lasting until 2015. He played 36 out of 38 top-flight fixtures that season, scoring four goals. On 3 December 2011, he was sent off for two bookings in a 4–2 loss to Blackburn Rovers at Ewood Park.

On 10 August 2012, after passing a medical at Melwood, Allen signed a long-term contract with Liverpool in a transfer deal worth £15 million, following Brendan Rodgers’ move to Anfield. Allen made his Premier League debut on 18 August 2012, starting in a 3–0 loss against West Bromwich Albion at The Hawthorns. He started Liverpool’s next match of the league campaign against Manchester City, where he was voted man of the match on the club’s official website by fans and journalists. He went on to win the Liverpool Player of the Month award for August 2012. Allen scored his first goal for Liverpool on 27 January 2013 in a 3–2 defeat to Oldham Athletic in the fourth round of the FA Cup. He scored his first European goal on 21 February in a 3–1 win over Zenit Saint Petersburg in the UEFA Europa League. On 20 March, it was announced Allen would be ruled out for the remainder of the 2012–13 season, with him requiring surgery on his left shoulder.

On 5 May 2014, Allen scored his first goal for Liverpool in the 2013–14 Premier League season with a header from a corner to give Liverpool the lead in a 3–3 draw against Crystal Palace at Selhurst Park. Allen played 26 times for Liverpool in 2013–14 as the side narrowly missed out on the Premier League title. In the 2014–15 season, Allen made 32 appearances as the side finished in sixth position. Allen was praised when he played the full 90 minutes in a 2–1 win against Manchester City, where he outplayed City star Yaya Touré. On 13 April 2015, Allen scored the second goal in a 2–0 win over Newcastle United, his first at Anfield.

Allen captained Wales for the first time in the absence of Ashley Williams through injury on 4 June 2014 against the Netherlands. He played throughout the nation’s successful qualification for UEFA Euro 2016. On 13 November 2015, in a 3–2 home loss to the Dutch, he had a penalty saved by Jasper Cillessen, but Joe Ledley scored from the rebound.

Allen is married to Lacey, with whom he has a son. Inspired by her involvement in animal welfare, he adopts hens to save them when they can no longer lay eggs. Allen’s brother Harry lost his hearing at age three due to meningitis, and Joe became ambassador for Action on Hearing Loss Cymru in March 2015. Harry also played football and became captain of the Welsh deaf futsal team.

Before the start of the 2015–16 season, Allen suffered an injury during one of the pre-season matches and was ruled out for a month. On 13 January 2016, he scored a last-minute equalizer in a 3–3 home draw against league leaders Arsenal. Thirteen days later, he scored the winning penalty in a shootout against Stoke City to send Liverpool to the 2016 League Cup Final. Allen was an unused substitute for Liverpool as they lost the final on penalties to Manchester City. However, Allen did play in the 2016 UEFA Europa League Final against Sevilla on 18 May 2016 in Basel, where despite initially taking the lead, Liverpool were defeated 3–1. At the end of the season, Allen expressed his desire to play regular football.

On 25 July 2016, Allen joined Stoke City on a five-year contract for a reported £13 million transfer fee. He made his Premier League debut for Stoke on 13 August 2016 in a 1–1 draw away at Middlesbrough. Speaking after his move to Stoke, Allen said he “had to move on” from Liverpool in order to receive regular playing time. He scored his first goal for Stoke on 24 September 2016 in a 1–1 draw against West Bromwich Albion. Allen then scored against Manchester United on 2 October as Stoke earned their first point at Old Trafford since 1980. Allen continued his goal scoring run with both goals in a 2–0 win against Sunderland earning Stoke their first victory of the 2016–17 season. In November 2016, Allen was included in the 40-man shortlist for the UEFA Team of the Year. He scored a vital winning goal against Crystal Palace on 11 February 2017. Allen made 39 appearances in 2016–17, scoring six goals, as Stoke finished in 13th position. Allen played 38 times in 2017–18, scoring four goals as Stoke suffered relegation to the Championship. Following relegation, Allen said he would be willing to stay with the club.

At Euro 2016, Allen set-up Aaron Ramsey’s goal in a 3–0 win over Russia on 20 June, which allowed Wales to top their group and advance to the knockout round of the tournament. Wales were eliminated following a 2–0 defeat to eventual champions Portugal in the semi-final on 6 July. Allen was named to the team of the tournament for his performances.

Allen signed new four-year contract with the Potters in June 2018. Allen was the only member of the squad to play every Championship game in 2018–19, as Stoke failed to mount a promotion challenge finishing in 16th. He scored six goals during the campaign most notably winning ones against Leeds United and his former club Swansea. Stoke began the 2019–20 season in poor form with Allen being sent-off against Bristol City on 14 September 2019. Allen scored in Michael O’Neill’s first match in a 4–2 win against Barnsley which lifted Stoke off the bottom of the table. Allen scored twice against Luton Town on 10 December 2019 in a 3–0 victory but came in for criticism after he celebrated by cupping his ears at the crowd. Allen was ruled out for the remainder of the season after suffering a achilles tendon rupture on 7 March 2020 playing against Hull City. In his absence Stoke managed to avoid relegation and finished in 15th position.