However, after that, Muggleton had a great deal of trouble retaining his place during a succession of injuries and much competition from Mark Laurie, Peter Wynn and Steve Sharp in Parramatta’s second row. By 1984, he was used chiefly as a reserve, and in 1985 Muggleton had a spell in the United Kingdom playing for Hull, alongside Sterling, in the then Rugby League First Division. That year, he played only one match in first grade for Parramatta after returning to Australia, but was recalled successfully in 1986 and, developing as a goalkicker, was able to keep his place and establish himself firmly in 1987 with the retirement of long-standing lock Ray Price.
A highlight that year was a booming field goal to beat Saint George 21 points to 20 with the last kick of the day.
However, in 1988 Muggleton was again out of favour and in his last two years he started only two first grade matches. After this, Muggleton turned to coaching, being most successful with North Sydney’s struggling President's Cup outfit in 1993 where he lifted them from twelfth to sixth.
Muggleton was formerly the defence coach with the Melbourne Rebels in the Super Rugby competition, serving from 2011 to 2013. Muggleton left the Rebels at the end of the season.
His last game as the defence coach of the Rebels was a home game against New Zealand franchise the Highlanders, a match that also turned out to be the last Rebels match for head coach Damien Hill and players James O"Connor, Gareth Delve, Cooper Vuna, Ged Robinson, Nick Phipps and Nic Henderson.
He previously coached Georgia at the 2011 Rugby World Cup. And, prior to that he was the defensive coach of the Llanelli Scarlets in south-west Wales. On 25 July 2014, Muggleton became the new Defence Coach for English rugby club Gloucester Rugby who compete in the Aviva Premiership
John has been the defence coach at the Parramatta Two Blues Rugby Club since November 2015.