The evidence suggests that Margaret was conventionally pious. That is, she followed religious practices that were common among the nobility of her time, and, insofar as we can tell, her beliefs would have been those shared by her contemporaries.

The content of her days was dictated by religious practice. The daily routine at court began with matins and a mass for the Virgin. William Say, dean of the king's chapel, recorded that Margaret rarely missed attending. Each day ended with evensong, followed by the Little Office of Our Lady, with prayers in between from a book of hours, and readings from such works as The Life of our Ladyby John Lydgate. As part of her regular observance, Margaret gave alms of 4d a day (a penny more than her yeomen received in wages), and on twenty-one ‘special feast days’ she made an offering of a gold coin. Only two of these special days were secular: the anniversaries of the deaths of Henry V and Queen Katherine. These days marked her religious year, beginning with the Annunciation of the Virgin on 25 March, two days after Margaret's birthday, and ending with the Purification of the Virgin on 2 February.

Margaret's devotion to the Virgin was a common feature of late medieval piety.

Her prayer roll, in Latin, pictured a wheel with seven spokes, all inscribed with prayers to the Virgin. At its center, the Virgin is shown, wearing a crown, with the Christ Child on her right arm and a white flower in her left hand. Beneath the wheel two angels support Margaret's arms, while Margaret kneels at a prie dieu gazing up towards the Virgin. In 1452 she commissioned a stained-glass window for a chapel at Westminster after fire had shattered its window and destroyed a jeweled statue of the Virgin as Our Lady of Pew (Pity) grieving over the body of Christ. The new window depicted King Henry and Margaret kneeling before the Virgin, with the queen's motto and the arms of the king, the queen, St George and St Edward. In 1453, when Margaret knew that she was pregnant, she traveled in gratitude and hope to the shrine of Our Lady of Walsingham.