The guidance follows the regulator's criticism of two evangelical churches last year for excessive salaries paid to their pastors.
Power Praise & Deliverance Ministries International in north London gave its pastor a £60,000 pay rise, from £15,464 to £75,359, despite the fact that he had spent half of the previous year abroad and his church was losing members.
And pastor Matthew Ashimolowo of Kingsway International Christian Centre was ordered to repay £200,000 to his organisation after a damning inquiry into "unauthorised trustee benefits".
The new model governing documents, which are not mandatory, still allow spiritual leaders to appoint trustees. The entire trustee board can also be the spiritual leaders of the church.
Kenneth Dibble, legal services director of the commission, said: "The aim of the model governing document is to ensure spiritual leaders can continue to play a key role in the management of church charities, controlling conflicts of interest without preventing them from providing essential services to churches as pastors."