The former Blues and Ospreys fly half passed the landmark with a second half conversion in a 30-15 win but saw his side forced to work hard for the victory at Sardis Road.
Craig Locke, Gareth James and Gavin Dacey all crossed in the first half but it could easily have been more for the home side as they wasted a number of further chances.
And although Quins refused to give up, Dylan Morgan and Ian Jones crossing in either half, Pontypridd were deserving winners with Huw Dowden adding their fourth try after half time.
Jack Maynard had given Quins the lead with a simple penalty with less than two minutes on the clock before Flanagan missed a simple chance to level things up – the usually reliable fly half striking the post with a penalty effort.
Despite trailing 3-0, the home side were dominating with their willingness to run the ball from deep a refreshing change from the aerial ping pong that is international rugby. And although centre Gary Williams let a clear try scoring opportunity slip by passing straight into touch with no one outside him, Pontypridd were not to be denied a second time.
Quick hands saw Locke go over in the corner with Flanagan seeing his conversion go over via the upright. Quins were seeing little of the ball and when Williams burst through a tackle inside his own half, another home score looked certain. He failed to find Matthew Nuthall outside him though and the chance was lost.
After wasting a number of opportunities, much to the home crowd’s annoyance, Quins then showed the league leaders how to be clinical. Out of nowhere, Morgan demonstrated his pace, escaping the covering defence to score in the corner. Maynard missed the conversion but his side had a one point lead.
Pontypridd continued to be wasteful, Nuthall seeing another effort ruled out for a forward pass but it seemed only a matter of time before they cut loose. And they did just that in the 15 minutes leading up to half time. Scrum half James dived over following a neat short line-out before Dacey added his side’s third score for a 17-8 interval lead.
The purple patch continued after the break, Flanagan kicking a simple penalty and converting Dowden’s push over try to break the 1,000 point mark. More importantly, Pontypridd now led 27-8 and were looking to cut loose in the final half hour.
Quins’ away record has been nothing short of exceptional this season though and despite facing a nine point deficit, they refused to give up. A Pontypridd scoring spree failed to materialise and prop Jones got the visitors back into it with a push over try. Maynard converted superbly and with 20 minutes left, the game was still in the balance.
Any sniff of a comeback was ended though when Haydn Pugh was yellow carded and the game became increasingly scrappy. And after replacing Flanagan, Simon Humberstone wrapped up Pontypridd’s win with a late penalty.
There remained a feeling though that they could,and perhaps should, have won by more.
