You don’t say what type of entities your organizations are.  I will assume that they are both nonprofit corporations or that, if one is a trust or an unincorporated association, your state law would allow you to convert it into a corporation.  A merger of two nonprofit corporations is pretty standard stuff.

You also don’t say what type of “nonprofit” you are, although I assume that your “nonprofit” isn’t charitable or you wouldn’t ask the question.  Presumably, the “nonprofit” will have to give up any non-charitable purpose to merge into the charity. Then the question will be whether your merged charity will qualify for the charitable exemption under state law.  Not every state gives charitable status to every entity that qualifies under the federal 501(c)(3) standards.  It may be worthwhile to ask the local assessors if the surviving corporation will qualify under your state requirements.  It would be a shame to go through all this effort if it doesn’t accomplish your goals.

You might also check to see if transferring title to the real estate would solve your problem.  Some states exempt property owned by a charity even if not used entirely for charitable purposes.  Transferring title might allow you to keep your separate entities and operations.