Margaret's biographer Turgot of Durham, Bishop of St. Andrew's, credits her with having a civilizing influence on her husband Malcolm by reading him narratives from the Bible. She instigated religious reform, striving to conform the worship and practices of the Church in Scotland to those of Rome. This she did on the inspiration and with the guidance of Lanfranc, a future Archbishop of Canterbury. She also worked to conform the practices of the Scottish Church to those of the continental Church, which she experienced in her childhood. Due to these achievements, she was considered an exemplar of the "just ruler", and moreover influenced her husband and children, especially her youngest son, the future King David I of Scotland, to be just and holy rulers.

"The chroniclers all agree in depicting Queen Margaret as a strong, pure, noble character, who had very great influence over her husband, and through him over Scottish history, especially in its ecclesiastical aspects. Her religion, which was genuine and intense, was of the newest Roman style; and to her are attributed a number of reforms by which the Church [in] Scotland was considerably modified from the insular and primitive type which down to her time it had exhibited. Among those expressly mentioned are a change in the manner of observing Lent, which thenceforward began as elsewhere on Ash Wednesday and not as previously on the following Monday, and the abolition of the old practice of observing Saturday (Sabbath), not Sunday, as the day of rest from labour (see Skene's Celtic Scotland, book ii chap. 8)." The later editions of the Encyclopædia Britannica, however, as an example, the Eleventh Edition, remove Skene's opinion that Scottish Catholics formerly rested from work on Saturday, something for which there is no historical evidence. Skene's Celtic Scotland, vol. ii, chap. 8, pp. 348–350, quotes from a contemporary document regarding Margaret's life, but his source says nothing at all of Saturday Sabbath observance, but rather says St. Margaret exhorted the Scots to cease their tendency "to neglect the due observance of the Lord's day."

She attended to charitable works, serving orphans and the poor every day before she ate and washing the feet of the poor in imitation of Christ. She rose at midnight every night to attend the liturgy. She successfully invited the Benedictine Order to establish a monastery in Dunfermline, Fife in 1072, and established ferries at Queensferry and North Berwick to assist pilgrims journeying from south of the Firth of Forth to St. Andrew's in Fife. She used a cave on the banks of the Tower Burn in Dunfermline as a place of devotion and prayer. St. Margaret's Cave, now covered beneath a municipal car park, is open to the public. Among other deeds, Margaret also instigated the restoration of Iona Abbey in Scotland. She is also known to have interceded for the release of fellow English exiles who had been forced into serfdom by the Norman conquest of England.

Margaret was as pious privately as she was publicly. She spent much of her time in prayer, devotional reading, and ecclesiastical embroidery. This apparently had considerable effect on the more uncouth Malcolm, who was illiterate: he so admired her piety that he had her books decorated in gold and silver. One of these, a pocket gospel book with portraits of the Evangelists, is in the Bodleian Library in Oxford, England.

Malcolm was apparently largely ignorant of the long-term effects of Margaret's endeavours, not being especially religious himself. He was content for her to pursue her reforms as she desired, which was a testament to the strength of and affection in their marriage.