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"
Lowry missed the first three cuts of his professional career, but had his first payday on 5 July, when he finished 50th at the Open de France ALSTOM. He had his best professional result in November 2009, when he finished 3rd in the Dunlop Phoenix Tournament in Japan. In January 2010, Lowry finished in fourth place in the Abu Dhabi Golf Championship, moving him into the top-100 of the Official World Golf Ranking.
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 28 January 2010, Lowry agreed a deal which would take him on a loan to Leeds United until 13 March 2010, joining his fellow Australian international teammates Patrick Kisnorbo and Neil Kilkenny. He made his debut for Leeds against Colchester United, playing left back for Leeds. After an impressive debut, Lowry suffered a minor injury and had to be substituted and replaced by Bradley Johnson after 70 minutes. After missing the FA Cup replay against Tottenham Hotspur due to not being eligible, Lowry returned to the Leeds starting lineup in the following game against Hartlepool United.
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.
OHL Classic at Mayakoba: Birdied two of his last three holes at the OHL Classic at Mayakoba to fire a final-round 67 and finish in 2nd place, one shot back of Patton Kizzire. In his first start at the event, opened with a bogey-free, 6-under 65 to sit three back of Kizzire's lead. Followed with three-consecutives rounds of 67 in rounds two through four, resulting in a score of 18-under 266. Due to inclement weather Saturday, played his final two rounds on Sunday.
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."'