The back row/second row forward has made 162 appearances for Welsh, scoring 12 tries, and was man of the match in the first leg of the Exiles' Championship final victory over the Cornish Pirates at Mennaye Field.
Mills, who took over the London Welsh captaincy at the start of the 2010/11 season, came through the academy at Bath and has also played for Llanelli RFC and Llandovery. He represented Wales at U16, U18, U19 and U21.
Although he joined the club in the summer of 2007, Mills enjoyed an unbeaten loan spell with the Exiles in January of that year, in which he made four appearances and scored one try, before making the switch to Old Deer Park permanent.
"I want to stay at London Welsh for as long as I can" said Mills. "I've been here for a long time already and I look forward to more success in the future.
"To see the club where it is now, its vision for the future and the calibre of players we have is fantastic. We now want to really establish ourselves in the Aviva Premiership - that's the next challenge.
"Having first come to London Welsh on loan when the club was still semi-professional and to then be part of it going full-time professional, reaching two Championship semi-finals and then finally getting promoted and reaching the Premiership has been hugely satisfying.
"At the beginning of the season people said we wouldn't get a point, but the work-rate and the hunger of the boys has been tremendous. It's been fantastic to be a part of that."
Prop forward Joly, 24, has made 12 appearances for London Welsh since joining the club from Bourgoin.
Joly began his career with Massey before spending four seasons at Stade Francais, where he gained Top 14 and Amlin Challenge Cup experience. He joined Bourgoin in 2011.
He represented France at Under U20 level in the Six Nations and was selected for the 2007 IRB Under-19 World Championships in 2007 in Belfast.
"I'm very happy to stay here for two more years. I'm very happy to continue to work with this team and with Lyn Jones," said Joly.
London Welsh head coach Lyn Jones said: "Jonathan has stepped up to Premiership level and has performed to a consistent standard. He has led by example as captain and has shown that when he's on the field he's a true Premiership player.
"Arthur has proved himself to be a very popular member of the squad, impressing all when he's played. He's still a young French prop who has a huge amount to learn about the game, but he's got the basics in place and he's going to prove a very good signing for London Welsh."
