One of Alan's most notable works was one he modeled after Boethius’ Consolation of Philosophy, to which he gave the title De Planctu Naturae, or The Plaint of Nature, and which was most likely written in the late 1160s. In this work, Alan uses prose and verse to illustrate the way in which nature defines its own position as inferior to that of God. He also attempts to illustrate the way in which humanity, through sexual perversion and specifically homosexuality, has defiled itself from nature and God. In Anticlaudianus, another of his notable works, Alan uses a poetical dialogue to illustrate the way in which nature comes to the realization of her failure in producing the perfect man. She has only the ability to create a soulless body, and thus she is "persuaded to undertake the journey to heaven to ask for a soul," and "the Seven Liberal Arts produce a chariot for her... the Five Senses are the horses". The Anticlaudianus was translated into French and German in the following century, and toward 1280 was re-worked into a musical anthology by Adam de la Bassée. One of Alan's most popular and widely distributed works is his manual on preaching, Ars Praedicandi, or The Art of Preaching. This work shows how Alan saw theological education as being a fundamental preliminary step in preaching and strove to give clergyman a manuscript to be "used as a practical manual" when it came to the formation of sermons and art of preaching.
Alan wrote three very large theological textbooks, one being his first work, Summa Quoniam Homines. Another of his theological textbooks that strove to be more minute in its focus, is his De Fide Catholica, dated somewhere between 1185 and 1200, Alan sets out to refute heretical views, specifically that of the Waldensians and Cathars. In his third theological textbook, Regulae Caelestis Iuris, he presents a set of what seems to be theological rules; this was typical of the followers of Gilbert of Poitiers, of which Alan could be associated. Other than these theological textbooks, and the aforementioned works of the mixture of prose and poetry, Alan of Lille had numerous other works on numerous subjects, primarily including Speculative Theology, Theoretical Moral Theology, Practical Moral Theology, and various collections of poems.
Alain de Lille has often been confounded with other persons named Alain, in particular with another Alanus (Alain, bishop of Auxerre), Alan, abbot of Tewkesbury, Alain de Podio, etc. Certain facts of their lives have been attributed to him, as well as some of their works: thus the Life of St Bernard should be ascribed to Alain of Auxerre and the Commentary upon Merlin to Alan of Tewkesbury. Alan of Lille was not the author of a Memoriale rerum difficilium, published under his name, nor of Moralium dogma philosophorum, nor of the satirical Apocalypse of Golias once attributed to him; and it is exceedingly doubtful whether the Dicta Alani de lapide philosophico really issued from his pen. On the other hand, it now seems practically demonstrated that Alain de Lille was the author of the Ars catholicae fidei and the treatise Contra haereticos.
In his sermons on capital sins, Alain argued that sodomy and homicide are the most serious sins, since they call forth the wrath of God, which led to the destruction of Sodom and Gomorrah. His chief work on penance, the Liber poenitenitalis dedicated to Henry de Sully, exercised great influence on the many manuals of penance produced as a result of the Fourth Lateran Council. Alain's identification of the sins against nature included bestiality, masturbation, oral and anal intercourse, incest, adultery and rape. In addition to his battle against moral decay, Alan wrote a work against Islam, Judaism and Christian heretics dedicated to William VIII of Montpellier.