In the 2012–13 season, Lowry regained his first team place, playing in the left-back and central defense positions until he missed one game after picking up a yellow card for the fifth time against Bristol City on 2 October 2012. After making his first team return as a left-back, Lowry then provided assist for the winning goal when he set up a goal for Chris Woods, in a 1–0 win against his former club, Leeds United on 18 November 2012. Lowry was then banned for two matches between 19 January 2013 and 25 January 2013 after picking up a yellow card for the tenth time this season. Lowry then He "curled a superb, dipping free-kick" to score from 35 yards (32 m) as Millwall beat Charlton Athletic 2–0 at The Valley on 16 March 2013. Lowry played in all matches in the run up to the Lions' FA Cup semi final against Wigan Athletic at Wembley, though he missed one match in the 4th round against his former club, Aston Villa. In late-April, Lowry was given a three match ban after being booked for the fifteenth time this season. Despite this, Lowry finished the 2012–13 season, making forty-five appearance and scoring once in all competitions.
Shell Houston Open: After opening with an 8-under 64 for a one-stroke lead on day one, added rounds of 71-67-70 to finish T3 at the Shell Houston Open. Erased a seven-shot deficit in the third round and started the final round three shots behind 54-hole leader Sung Kang, but a final-round 70 saw him finish four strokes behind winner Russell Henley. With 27 birdies on the week (tied for most with Henley), marked his most birdies in a single event.
In July 2011, Fowler tied the 54-hole lead at the AT&T National, but an early double bogey on Sunday derailed his opportunity for his first PGA Tour win. Two weeks later Fowler finished tied for 5th in The Open Championship at Royal St George's. In August, Fowler finished in a tie for second at the WGC-Bridgestone Invitational behind winner Adam Scott, lifting him to 28 in the world rankings.
At the 2016 U.S. Open at Oakmont Country Club near Pittsburgh, Lowry shot 65 (−5) in the third round for 203 (−7) and a four-stroke advantage over Dustin Johnson and Andrew Landry at the 54-hole stage. The 65 was Lowry's joint career best round at a major championship. Due to weather delays on Thursday, the third round was not completed until early on Sunday, and Lowry birdied two of his remaining four holes to extend his two stroke overnight lead to four. In the final round he was in contention for the title, within one shot of Dustin Johnson after 12 holes, before three consecutive bogeys on holes 14, 15 and 16 ended his chances. He finished the tournament tied for second place, with a final round score of 76.
Lowry started for Leeds in the Football League Trophy Northern Area Final, second leg game against Carlisle United, in which the game was lost with Lowry missing the decisive penalty in sudden death in the penalty shootout. After the game it appeared as though Lowry was attacked by a set of Carlisle supporters who had invaded the pitch. After starting every game for Leeds Lowry was dropped from the Leeds squad for the match against Brentford after suffering an injury, before returning to Villa when his loan spell ended. On 25 March 2010 Lowry re-signed for Leeds for a second loan spell, with his loan lasting until the end of the season. Lowry started at left back for Leeds against Norwich City on his return to the club, a match Leeds went on to lose 1–0 in injury time. Lowry didn't overley impress the Leeds fans in his loan spell at Leeds, with him being mostly played out of position at Left back for the entire spell, he was substituted for Jonathan Howson in the final game of the season against Bristol Rovers with 1–0 down at the time, but his loan spell ended on a high as Leeds were promoted in 2nd place after scoring two goals to go on and beat Bristol Rovers and secure promotion to The Championship.
Lowry was the 2007 Irish Amateur Close Champion, defeating Niall Turner 4 & 3 in the final. While still an amateur in May 2009, he won The Irish Open on the European Tour, defeating Robert Rock on the third hole of a sudden death playoff. The win, on his tour début, made him just the third amateur to win on the European Tour, following Danny Lee earlier in the 2009 season, and Pablo Martín in 2007. Lowry shot a 62 to equal the lowest ever by an amateur on the circuit and led from the second round onwards.
After a tie for fifth at the Masters in April, Fowler had his best finish of 2014 at the U.S. Open at Pinehurst No. 2 in North Carolina. Fowler was runner-up with Erik Compton at −1, best finishes for both at a major, but they were eight strokes behind champion Martin Kaymer. Fowler had another second-place finish, at the Open Championship at Royal Liverpool Golf Club in Hoylake, England. He began the final round six strokes behind Rory McIlroy and finished the day tied for second with Sergio García at −15, two strokes behind McIlroy. At the next major in August, the PGA Championship, Fowler, Phil Mickelson, Henrik Stenson, and McIlroy battled for the title on a rain-soaked Valhalla Golf Club, near Louisville. Despite holding the lead for a good portion of the day, Fowler tied for third. He was only the third player, along with Jack Nicklaus and Tiger Woods, to have finished in the top 5 in all four majors in one calendar year, but the first not to win (Jordan Spieth became the fourth player in 2015). Fowler had 10 top-10 finishes during the 2013–14 season. His 8th-place finish at The Tour Championship moved him to 10th in the world golf rankings.
On 23 November 2011, Lowry was again loaned out to play in the Championship, this time to Millwall until 3 January 2012. He followed Aston Villa team-mate Nathan Baker who also signed on loan for Millwall two days earlier. Lowry made his Millwall debut three days later, where he played 90 minutes, in a 0–0 draw against Crystal Palace. His impressive display at Millwall soon earned a loan extension. Weeks later on 13 January 2012, Lowry was sent-off in the 22nd minutes after stamping on Nikola Žigić, which saw Millwall lose 6–0. Three years on after signing for Birmingham City, Lowry stated, quoting: "Whatever club I play for I fully commit to that club at the time. I play with my heart on my sleeve. Sometimes in the past I have gone overboard but I was a younger player then, I have learned a lot from these types of experiences. But I am an aggressive player, that’s the way I like to play and I can’t change the way I play. I will use my experience now and be a bit more clever."'
After finishing fifth in the Hyundai Tournament of Champions in Hawaii, Fowler claimed his first victory of 2016 in the Abu Dhabi HSBC Golf Championship on the European Tour. He shot a final round of 69 to finish one clear of Belgium's Thomas Pieters. Two weeks later, Fowler was in contention to win again but lost out to Japan's Hideki Matsuyama in a playoff at the Waste Management Phoenix Open. On March 7, Fowler sparked fantastic scenes after sinking a hole-in-one with fellow tour pro Luke Donald's pitching wedge to win $1 million for Ernie Els' charity, Els for Autism.
Lowry made his professional debut in the 2009–10 UEFA Europa League in an away fixture at Rapid Vienna. On 17 September 2009, Lowry signed a three-month loan deal with Football League Championship side Plymouth Argyle. Lowry made his Plymouth Argyle debut on 19 September 2009, playing 90 minutes, in a 3–1 loss against Newcastle United. He played 13 league games for Plymouth during his loan spell, where he impressed many and was recalled by Villa who required Lowry's services as cover after some injuries to defenders.
Enjoyed a stellar rookie season, with seven top-10 finishes and a 32nd-place finish in the FedExCup standings that led to him winning PGA TOUR Rookie of the Year honors. Finished inside the top 30 on the money list to qualify for the Masters and the U.S. Open. Played in first three Playoff events, slipping from 21st to 32nd and out of the TOUR Championship.
In the 2013–14 season, Lowry suffered a minor thigh strain in the club's pre-season friendly. Despite this, Lowry remained in the first team under the new management of Steve Lomas until he received a straight red card after a foul on Will Hughes, in a 5–1 loss against Derby County on 14 September 2013. After serving a three match ban, Lowry remained on the bench without playing for four matches Lowry made his first team return on 2 November 2013 when he came on as a substitute for Scott Malone against Burnley. However, his return, after spending two months without playing, was a disastrous when he scored an own goal, which saw Millwall drew 2–2. After this, Lowry was out of the first team, demoted to the substitute bench between mid-November and mid-December until he made his return on 26 December 2013, in a 4–0 loss against Watford. On 28 January 2014, Lowry was sent-off for the second time this season in the late-minutes against Sheffield Wednesday after fighting with Giles Coke, who also was sent-off as well, with both side drew 1–1. After serving a four match ban, Lowry was in the first team throughout February and March until he suffered a foot injury that kept him out for the remainder of the season. Lowry went on to finish the 2013–14 season, making twenty-two appearance.
Lowry received his first call-up to the full Australia squad for a friendly against the Netherlands in Sydney and the Asian Cup qualifier against Oman in Melbourne in October. He did not play in either match. On 11 May 2010 he was selected as part of Pim Verbeek's 30-man provisional squad for the 2010 World Cup, and travelled to South Africa, but was not included in the final 23-man World Cup squad. Lowry was named in Han Berger's 18-man squad for an August 2010 friendly against Slovenia, but he did not appear in the match.
The Barclays: Held a one-stroke lead over Patrick Reed after 54 holes at The Barclays in the FedExCup Playoffs, before a double bogey-birdie-bogey finish on Nos. 16-18 resulted in a T7 at 6-under 278 with Jason Kokrak and Ryan Moore. Fowler went bogey free at Bethpage Black from the 10th hole in round one until the 11th hole in the final round, a span of 55 holes. His 55-consecutive holes without a bogey became a personal best on the PGA TOUR, besting 53 from the 2010 Memorial Tournament. This streak also marked the longest recorded in Barclays history since hole information began in 1983. Ian Poulter had the longest with 45 in 2010. The finish marked his third top-10 showing in his last four starts in the event (T9/2013, T9/2014).