While serving a suspension, Lowry signed a two-and-a-half-year permanent deal to Millwall for an undisclosed fee on 27 January 2012. Lowry then made his first appearance for the club since joining Millwall permanently, playing 90 minutes, in a 2–1 loss against rivals' West Ham United on 4 February 2012. Right way through March, Lowry was sidelined with ankle injury that kept him out for weeks. After making his first team return against Cardiff City, in a 0–0 draw on 31 March 2012, Lowry scored his first Millwall goal, which he scored the only goal in the game, in a 1–0 win over Coventry City on 17 March 2012. Lowry finished his 2011–12 season, making twenty-two appearance and scoring once.
In September, he signed a clothing deal with Puma. In the same month, he was also chosen as a captain's pick for the U.S. Ryder Cup team. At age 21 years and 9 months when the matches began, Fowler became the youngest U.S. Ryder Cup player of all time, and only European Sergio García was younger when he made his Ryder Cup debut in 1999. Fowler forfeited a hole during foursomes competition on the first match day because of a rules violation, by taking a permissible free drop from muddy conditions in an improper location, a mistake U.S. captain Corey Pavin attributed to Fowler's inexperience. On the final day of the competition in his singles match against Edoardo Molinari, Fowler birdied the last 4 holes to halve the match after having been 4 down after 12 holes.
At the first FedEx Cup playoff event of the season, The Barclays, Fowler went into the final round leading the event by one stroke. He endured a difficult final round, shooting a two-over-par 74. His challenge was ended with a double-bogey at the 16th hole that put him four strokes behind playing partner Patrick Reed. He went on to finish T7, three strokes behind the winner Reed. As a result of this, Fowler also failed to secure his automatic Ryder Cup spot, which he would have done with a top-three finish. Fowler moved up from 28th to 16th in the FedEx Cup standings with this result.
THE PLAYERS Championship: A week after collecting his first PGA TOUR victory, nearly became the first player since David Duval (1997) to post first two TOUR victories in back-to-back weeks, finishing T2 at THE PLAYERS, two strokes behind winner Matt Kuchar. Holed a birdie attempt from 21 feet, 7 inches on the par 3 17th in the final round to move to 11-under but couldn't convert a 7-foot, 7-inch birdie on No. 18 that would have given him the clubhouse lead at 12-under. Recorded his fifth career runner-up finish on TOUR in his 73rd start. His T2 performance came in his third start at THE PLAYERS and first in which he made the 36-hole cut. Moved into contention with a 66 in the third round, a career low at TPC Sawgrass. Entered the final round three shots off the 54-hole pace.
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.
Hyundai Tournament of Champions: Finished T6 in a Monday-start-Tuesday-finish event, the season-opening, 54-hole Hyundai Tournament of Champions. The event "started" twice during the regularly scheduled first round Friday and later Sunday, but both times PGA TOUR rules staff halted play due to unplayable windy conditions and subsequently voided all scores that had taken place. As the first player off the tee, he ended up hitting three "opening" shots of the season.
As for the workouts he’s doing, DeChambeau is continuing work he’s done with Greg Roskopf, whose system focuses on making people stronger where they are weak, particularly at extraneous points in their muscular system. In other words, there are likely points in the golf swing — in various golf movements — where DeChambeau isn’t as strong as he could be, hence the more work and weight. If he has already ascended to 220 in a matter of weeks, 230 should follow soon. Stay tuned.
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.
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).