Mark Harte and Adrian O'Donnell will take the reins at Ballinderry once Pomeroy's involvement in the All-Ireland club IFC ends.
The pair, who guided Pomeroy to Tyrone and Ulster IFC honours in recent months, will take over from Martin McKinless, who stepped down in the wake of the Shamrocks' Derry SFC semi-final defeat to Slaughtneil.
Ballinderry chairman Pearse Cullen is quoted in the Ulster Herald as saying: "Ballinderry Shamrocks are delighted to announce the appointment of Mark Harte and Adrian O'Donnelly as our joint senior managers for the forthcoming season.
"Mark and Adrian will continue in their current role as senior team managers with Pomeroy until the conclusion of their current All-Ireland campaign.
"Mark and Adrian have asked that no further media enquiries are directed towards them in respect of their new appointment at this time. Their entire focus understandably is on their preparations for an All-Ireland Intermediate club semi-final in January 2017."