The merger will create a new body with a turnover of £50m and 2,000 staff.
The respective trustee boards have agreed to the plans, pending a final decision in January 2007. The two organisations are currently working on legal and financial preparations and employee consultations.
John Grooms Housing Association will remain independent, but will work in partnership with the merged body. A spokeswoman for all the charities said the three organisations had been talking about pooling their resources for some time so that disabled people could benefit from more services and more effective advocacy and campaigning.
John Grooms and Shaftesbury have historical links. Shaftesbury's founder, the seventh Earl of Shaftesbury, was the first president of John Grooms.
The working title of the project is Grooms-Shaftesbury, but the spokeswoman said it was premature to announce launch plans until the merger was formally confirmed.
Both of the organisations describe themselves as Christian, but Shaftesbury is more explicit about its religious orientation. It is also the larger, with 1,400 staff and a turnover of £30m.