The administration of its affairs was intrusted to a governor, deputy, and eighteen assistants, who were annually, on the last Wednesday of Easter term, to be elected by the freemen or members of the corporation, and to meet once a month or oftener "for despatching such business as concerned the company or plantation." Four times a year the governor, assistants, and all the freemen were to be summoned to "a greate generall, and solemne assemblie," and these "greate and generall courts" were invested with full power to choose and admit into the company so many as they should think fit, to elect and constitute all requisite subordinate officers, and to make laws and ordinances for the welfare of the company and for the government of the plantation.
The company was given the power to transport to its American territory all persons who should go willingly, but the corporate body alone was to decide what liberties, if any, the emigrants should enjoy.

In fact, the only restrictions in the charter upon the company and its court of assistants were that they should license no man "to rob or spoil," hinder no one from fishing upon the coast of New England, and pass "no law contrary or repugnant to the lawes and statutes of England." Matthew Cradock was named in the charter the governor of the company.
One of the first steps taken by the company under the new charter was to organize a temporary local government for the colonists in Massachusetts.

This was to consist of a governor, a deputy governor, and thirteen councillors, of whom seven were to be named by the company, three were to be chosen by these seven and the governor, and three more were to be appointed by the "old planters" found in Massachusetts at the arrival of Endicott.

Land was allotted on a plan like that adopted by the London Company: each shareholder was to have two hundred acres for every L50 that he invested, and if he settled in that country, fifty more for himself and fifty more for each member of his family.[11] A letter of instructions was draughted, April 17, to Governor Endicott, in which mention was made of the negotiations with Oldham, and orders given to effect an occupation of the territory covered by his grant from John Gorges.

This letter was sent off by a special ship which reached Salem June 20, 1629, and Endicott promptly despatched three brothers of the name of Sprague, and a few others, who planted themselves at Mishawum, within the disputed territory, where they found but "one English palisadoed and thatched house wherein lived Thomas Walford, a smith." Other emigrants followed, and there, in July, was laid out by Endicott a town which was named Charlestown.
This practically ended the difficulty with Oldham, who was kept in the dark till the ship sailed from England, and was then told by the company that they were determined, on advice of counsel, to treat his grant as void.