Dascombe, who had spells with Martin Pipe, Ralph Beckett and Mike de Kock before striking out on his own, has enjoyed a successful spell at the helm.
His biggest success came through Brown Panther, winner of the Irish St Leger in 2014, while he has also tasted victory at Royal Ascot, trained popular sprinter Kachy and won the Ayr Gold Cup with Angel Alexander.
In a statement Owen said: "After more than 12 years as trainer, Tom Dascombe will be leaving Manor House Stables in the new year.
"We have shared many great times and races together and created memories that will last a lifetime.
"I would like to place on record my own personal thanks for all his hard work and support over the years. We part on great terms and everyone at MHS will miss him and wishes him the very best for the future."
The former England striker added: "Colin Gorman and the rest of the MHS team will naturally oversee things once Tom departs and it will be very much business as usual until we appoint Tom's replacement."