She was forced to release the archbishop to consolidate her position as regent, but resolved the conflict of power between the church and the crown by banishing the archbishop from the kingdom: the question of the church's autonomy from the Danish crown was not settled until some years after her son's maturity, but Margaret continued to negotiate with the Pope until she solved the matter, even after her mandate as regent was terminated.

[6] She was also faced with having to protect her son's right to the throne against the claims of the sons of her brother-in-law Abel of Denmark, whose claims to the throne was raised by Abel's widow Matilda of Holstein, as well as given the responsibility of the four daughters of her other brother-in-law Eric IV of Denmark, Sophia, Ingeborg, Jutta and Agnes.

[7] Her son's succession overrode the rights of the descendants of earlier monarchs, counter to the dictates of agnatic seniority.

[8] She was not able to prevent the marriage alliances between Abel's widow Matilda of Holstein and Birger Jarl, or Eric IV's daughters Sophia and Ingeborg to the kings of Norway and Sweden, but she was able to prevent Eric IV's remaining daughters Jutta and Agnes from similar marriage alliances by placing them in the convent St. Agnes' Priory, Roskilde.

Margaret retired as regent in 1264, when her son was declared an adult, and she officially settled with her own court in her personal residence Nykøbing Slot on Falster.

[7] In 1266, her son the king granted her the rulership of Danish Estonia, and made her ruling countess of the province for life.