The "composite Magdalene" was never accepted by the Eastern Orthodox churches, who saw only Mary the disciple, and believed that after the Resurrection she lived as a companion to the Virgin Mary, and not even in the West was it universally accepted. The Benedictine Order always celebrated Mary of Bethany together with Martha and Lazarus of Bethany on 29 July, while Mary Magdalene was celebrated on 22 July. Not only John Chrysostom in the East (Matthew, Homily 88), but also Ambrose (De virginitate 3,14; 4,15) in the West, when speaking of Mary Magdalene after the resurrection of Jesus Christ, far from calling her a harlot, suggest she was a virgin. In 1518, on the brink of the Protestant Reformation, the leading French Renaissance humanist Jacques Lefèvre d'Étaples wrote arguing against the conflation of Mary Magdalene, Mary of Bethany and the unnamed sinner in Luke. There was a flurry of books and pamphlets, most opposing Lefèvre d'Étaples, but others supporting him. In 1521 his views were formally condemned by the theology faculty of the Sorbonne, and debate died down, overtaken by the larger issues raised by Martin Luther. Although Protestant Theologians and biblical commentators such as John Calvin rejected the composite Magdalene. for Luther and Zwingli Mary Magdalene is the composite Magdalene of medieval tradition,

During the Counter Reformation and Baroque periods (late 16th and 17th centuries), the cult of Mary Magdalene saw a great, new popularity as the Catholic Church publicized her as an attractive, persuasive model of repentance and reform, in keeping with the goals of the reform Council of Trent (1545–63). Numerous works of art and theater featuring the tearful penitent Magdalene appeared in the 17th century. As part of this new attention to the cult of the Magdalene, in 1600, her relics were placed in a sarcophagus commissioned by Pope Clement VIII, the head being placed in a separate reliquary. The relics and free-standing images were scattered and destroyed at the Revolution. In 1814, the church of La Sainte-Baume, also wrecked during the Revolution, was restored. In 1822, the grotto was consecrated afresh. The head of the saint now lies there and has been the centre of many pilgrimages.

The 1549 Book of Common Prayer had on July 22 a feast of Saint Mary Magdalene, with the same Scripture readings as in the Tridentine Mass and with a newly composed collect: "Merciful father geue us grace, that we neuer presume to synne through the Example of anye creature, but if it shall chaunce vs at any tyme to offende thy dyuine maiestie: that then we maye truly repent, and lament the same, after the Example of Mary Magdalene, and by lyuelye faythe obtayne remission of all oure sinnes: throughe the onely merites of thy sonne oure sauiour Christ." The 1552 edition omitted the feast of Saint Mary Magdalene, which was restored to the Book of Common Prayer only after some 400 years.

In that period, the description "penitent" was added to the indication of her name on her feast day, 22 July. It had not yet been added at the time of the Tridentine Calendar of 1569 and is no longer found in the present General Roman Calendar but, once added, it remained until the General Roman Calendar of 1960. Mary Magdalene thus became a symbol of repentance from the vanities of the world. The Gospel reading in the Tridentine Mass was Luke 7:36–50 (the sinful woman anointing the feet of Jesus), while in the present version of the Roman Rite of Mass it is John 20:1–2, 11–8 (meeting of Mary Magdalene with Jesus after his resurrection). St. Mary Magdalene was the patron of Magdalen College, Oxford, and Magdalene College, Cambridge (both colleges pronounce her name as "maudlin"). In contrast, her name was also used for the Magdalen Asylums, institutions for "fallen women".

Edgar Saltus's historical fiction novel Mary Magdalene: A Chronicle (1891) depicts her as a heroine living in a castle at Magdala, who moves to Rome becoming the "toast of the tetrarchy", telling John the Baptist she will "drink pearls... sup on peacock's tongues".

The Gospel of Mary was probably written over a century after the historical Mary Magdalene's death. The gospel does not claim to have been written by her and its author is, in fact, anonymous. Instead, it received its title because it is about her. First discovered in 1896, the Gospel of Mary provides important information about the role of women in the early church, although it is missing six pages from the beginning, and four from the middle. It is usually dated to about the same period as that of the Gospel of Philip.

The Gospel of Philip, dating from the second or third century, survives in part among the texts found in Nag Hammadi in 1945. In a manner very similar to John 19:25–26, the Gospel of Philip presents Mary Magdalene among Jesus' female entourage, adding that she was his koinônos, a Greek word variously translated in contemporary versions as partner, associate, comrade, companion:

The Common identification of Mary Magdalene with other New Testament figures was omitted in the 1969 revision of the General Roman Calendar, with the comment regarding her liturgical celebration on 22 July: "No change has been made in the title of today's memorial, but it concerns only Saint Mary Magdalene, to whom Christ appeared after his resurrection. It is not about the sister of Saint Martha, nor about the sinful woman whose sins the Lord forgave (Luke 7:36–50)." Elsewhere it said of the Roman liturgy of 22 July that "it will make mention neither of Mary of Bethany nor of the sinful woman of Luke 7:36–50, but only of Mary Magdalene, the first person to whom Christ appeared after his resurrection". Mary of Bethany's feast day and that of her brother Lazarus is now on 29 July, the memorial of their sister Martha.

In his apostolic letter Mulieris Dignitatem ("On the dignity and vocation of women", parts 67–69) dated 15 August 1988, Pope John Paul II dealt with the Easter events in relation to the women being present at the tomb after the Resurrection, in a section entitled 'First Witnesses of the Resurrection':

In 1998, Ramon K. Jusino proposed an unprecedented argument that the "Beloved Disciple" of the Gospel of John is Mary Magdalene. Jusino based his argument largely on the Nag Hammadi Gnostic books, rejecting the view of Raymond E. Brown that these books were later developments, and maintaining instead that the extant Gospel of John is the result of modification of an earlier text that presented Mary Magdalene as the Beloved Disciple. Richard J. Hooper does not make the Jusino thesis his own, but says: "Perhaps we should not altogether reject the possibility that some Johannine Christians considered Mary Magdalene to be 'the disciple whom Jesus loved'." Esther A. de Boer likewise presents the idea as "one possibility among others", not as a definitive solution to the Problem of the identity of the anonymous disciple. A theological interpretation of Mary as the Magdala, The Elegant Tower and certain churches honor her as a heroine of the faith in their teachings.

Ki Longfellow's novel The Secret Magdalene (2005) draws on the Gnostic gospels and other sources to portray Mary as a brilliant and dynamic woman who studies at the fabled library at Alexandria, and shares her knowledge with Jesus.

The "Gospel of Jesus' Wife", a Coptic papyrus fragment unveiled in 2012, presents Jesus as speaking of his wife: "My wife ... she will be able to be my disciple." If genuine, it appears to date to around the 6th to 9th centuries AD, and would suggest that some Egyptian Christians of that period believed that Jesus was married. Although it does not contain the name of Mary Magdalene, there has been speculation that she is the woman referred to. However, there is substantial scholarly concern about the fragment's authenticity, with a number of scholars regarding it as a modern forgery.

The 13th-century Cistercian monk and chronicler Peter of Vaux de Cernay claimed it was part of Catharist belief that the earthly Jesus Christ had a relationship with Mary Magdalene, described as his concubine:

In The Lost Gospel, in 2014 Simcha Jacobovici and Barrie Wilson proposed a reading of Joseph and Aseneth using Syriac typology. On this interpretation, Joseph is a surrogate for Jesus, Aseneth for Mary Magdalene. When decoded in this fashion, the narrative relates their courtship, marriage and offspring. Following symbolism in the work, Jesus is depicted as Helios, Mary Magdalene as Artemis. Redemption is based on sacred marriage, the unification of the genders as per Gnostic writings, not on a sacrificial atonement theology.

On 10 June 2016, the Congregation for Divine Worship and the Discipline of the Sacraments issued a decree which elevated Mary's liturgical commemoration from an obligatory memorial to a feast day, like that of most of the Apostles (Peter and Paul are commemorated with a solemnity). The Mass and Liturgy of the Hours (Divine Office) remained the same as they were, except that a specific preface was added to the Mass to refer to her explicitly as the "Apostle to the Apostles".

According to Robert Kiely, "No figure in the Christian Pantheon except Jesus, the Virgin Mary, and John the Baptist has inspired, provoked, or confounded the imagination of Painters more than the Magdalene". Apart from the Crucifixion, Mary was often shown in scenes of the Passion of Jesus, when mentioned in the Gospels, such as the Crucifixion, Christ Carrying the Cross and Noli me Tangere, but usually omitted in other scenes showing the Twelve Apostles, such as the Last Supper. As Mary of Bethany, she is shown as present at the Resurrection of Lazarus, her brother, and in the scene with Jesus and her sister Martha, which began to be depicted often in the 17th century, as in Christ in the House of Martha and Mary by Velázquez.

These claims, however, have been contested by scholars. The text of Zacharias tells the familiar story of Joseph and Aseneth based on the life of the patriarch Joseph, son of Jacob. When Joseph was released from prison, he got married to Asenet, daughter of a priest of Heliopolis. The text itself is not a Gospel or a lost text as suggested by Wilson and Jacobovici; instead it is a well known text, discussed since the nineteenth century. Robert Cargill writes his review:"The book’s methodology is highly problematic. Scholars won’t reject Mr. Jacobovici’s findings because of some “theological trauma” or a confessional, apologetic Desire to preserve the Jesus described in the Bible... The Problem is not a theological one, it is one of scholarship, methodology, and the (mis)use of evidence. Scholars won’t reject Mr. Jacobovici’s claims because they want to defend Christianity, scholars will reject Mr. Jacobovici’s speculations because he engages in circular reasoning, lacks evidence, breaks any number of rules of textual criticism, and engages in ...'speculation wrapped in hearsay couched in conspiracy masquerading as science ensconced in sensationalism slathered with misinformation'. .