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.
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.
Hero World Challenge: After beginning the final round seven strokes out of the lead, closed with a tournament-record, personal-best 11-under 61 to win the Hero World Challenge by four strokes over Charley Hoffman. With a winning score of 18-under 270, won at the age of 28 years, 11 months and 20 days. His 61 topped the previous Hero World Challenge course record of 62, set by Albany resident Justin Rose during the final round in 2015. Prior to his 61, the previous low final-round score by a Hero World Challenge winner was 64, set on three occasions and most recently by Luke Donald in 2005. Opened his final round with seven birdies before making his first par on the par-4 eighth hole. No player has had as long a streak of birdies in an official PGA TOUR event to open a round since Joe Durant started round four of the 2005 Honda Classic with seven in a row. Added a birdie on the ninth hole to make the turn with an 8-under 28, turning a seven-stroke deficit into a two-stroke lead. His final round included 11 birdies, two more than his benchmark of nine birdies in official PGA TOUR events (final round of the Quicken Loans National in 2017). Finished the week at Albany Golf Club with 30 birdies, three more than his highest total in official PGA TOUR events (27 – 2017 Houston Open). Recorded his sixth top-six finish at the event in his sixth start (1/2017, T3/2016, 3/2015, T6/2014, T4/2012, T6/2011).
2019 Open Champion Shane Lowry, compared to Tommy Fleetwood, is on the other side of the spectrum in regards to brand loyalty. He is Cleveland/Srixon in 12 clubs including the ball with the only two exceptions being the TaylorMade M4 3-wood and his Odyssey Putter. In this case, that makes sense, those clubs seem to be a challenge to swap, especially the 3-wood, and Cleveland/Srixon isn’t really known for putters on the PGA Tour.
The Open Championship: Enjoyed his best finish among seven major championship starts, with a T5 at The Open Championship at Royal St. George's. Opened with three par-or-better rounds to enter the final round three strokes behind Darren Clarke. Closed with a 2-over 72 in windy conditions to finish tied with fellow Americans Chad Campbell and Anthony Kim.
Lowry made his debut for the Glory on 30 January 2016, starting against Melbourne Victory. Lowry then scored his first Perth Glory goal on 20 February 2016 when he scored a header in the 41st minutes, to give Brisbane Roar a thrashing with a 6–3 win for Perth Glory. Throughout the 2015–16 season, Lowry established himself in the starting eleven and formed a central defense partnership with Alex Grant, as he made ten appearance for Perth Glory in his first half of the season.
On 27 January 2016, Lowry returned to Australia after a decade away from Australia when he signed a two-and-a-half-year deal with A-League side Perth Glory. Upon joining Perth Glory, Lowry said of the move, quoting: "I've got a lot of experience behind me now and I want to use it to guide the young lads who are in this young squad. I've spent 11 years in England and it's shaped my football over there and I'm really happy to be here and get stuck into the games"