The fly half, who has played regional rugby with both the Blues and the Ospreys, returned to Sardis Road at the start of this season after a spell with Bridgend Ravens.
And despite not starting week in week out, Flanagan's nerveless goal kicking helped Pontypridd to a first ever double. It also saw him crowned as the Premiership's top points scorer at Tuesday night's end of season awards evening at the Millennium Stadium.
"It's been a great return for me personally coming back to Pontypridd," said Flanagan.
"I could see from the outside how hard the group had been working, coming as close as they could have done to winning the double. We've done it now and this season is just reward for the players who have stuck at it over three years.
"There were a couple of targets I set myself - getting my 100th cap, reaching 1,000 points for the club, winning the double and winning this award.
"I seem to have ticked every box and next season is now about staying at that level of performance."
For a man who kicked the Blues to a Heineken Cup win over Stade Francais, Flanagan isn't short of big match experience. That know-how was in evidence throughout the season, Pontypridd's SWALEC Cup quarter-final win over Ebbw Vale a particularly good example.
Trailing by a single point, Flanagan needed to convert Chris Dicomodis' try from the touchline to send his team into the next round. He did just that and the rest, as they say, is history.
"The award is a bonus for the group really," said Flanagan modestly.
"I've had quite a few important kicks throughout my career not just this season.
"The conversion against Ebbw Vale was important but the penalty before that was equally important even though it was simple. Without that, we wouldn't have won."
After the quarter final win against the Steelmen, Pontypridd went on to defeat Neath in the final at the Millennium Stadium before a convincing win over Llanelli saw them crowned Principality Premiership kings.
"The Ebbw Vale kick stands out and there was a drop goal in the cup and the conversion against Leinster in the British & Irish Cup," added Flanagan.
"Even though it was a missed kick, the feeling of beating Leinster at home sticks in my mind.
"I get plenty of shots at goal playing for a successful team so any success is down to the other 14 players on the pitch."