Maimonides’ position on the soul is very complex and this subject remains of the more controversial topics of Jewish intellectual history. Certainly in his commentary to the Mishnah, Maimonides includes the belief in bodily resurrection among the basic tenants of faith listed in his famous Thirteen Articles of Belief.
However, in Maimonides’ most mature work, the philosophical tract known as “The Guide to the Perplexed,” the great philosopher stresses the belief in the soul’s immortality and says nothing about physical resurrection.
One might wonder: How consistent is Maimonides? Actually, one could answer that it all depends upon the specific target audience he was trying to educate. For traditionalists, Maimonides endorses the standard orthodox beliefs that everyone knew. This point is visibly clear in his famous essay on Resurrection where he defends himself against the accusation he “denied the existence of physical resurrection.”
Many scholars doubt whether Maimonides was really being truthful when he composed his letter; others think the text may have been a forgery. On the other hand, Maimonides sometimes expresses sentiments that he would never publicly endorse; the belief in resurrection could be one such example.
Maimonides reveals his most personal theological views regarding resurrection in his Guide to the Perplexed–not so much by what he says, but by what he does not say! If I understand Maimonides correctly, I think he never really denies resurrection; rather, he gives it a new understanding. Resurrection simply means that the soul is reborn into the world of Eternity after the body perishes in this world.
Maimonides’ sophisticated grasp of anthropomorphism and his rejection of scriptural literalism strongly indicates that the greatest Jewish philosopher of the medieval era also viewed resurrection as a metaphorical truth. One must remember that Maimonides was the first Jewish thinkers to engage in a process of de-mythologizing Scriptures, which often speaks in mytho-poetic language that can best be understood as metaphor.
If this conjecture is correct, Maimonides’ view certainly fits a more modern way of viewing faith; briefly stated, resurrection does not suspend the laws of nature, rather, it refers to a metaphysical journey where the soul returns to its original state of being. Physical death does not have the final word on the soul’s existence. By the same token, Maimonides (and especially Gersonides after him) generally interprets supernatural miracles of the Bible in naturalistic terms. Natural law within the universe remains inviolate.
In contrast, Maimonides’ Mishneh Torah essentially does not deal with philosophic ideas but rather with practical halacha and the sundry principles of faith. Maimonides writes that in the olam ha-ba (“World to Come” also known as the “Afterlife”), “There are no bodies, but only the souls of the righteous, without body, serving as the angels of God. Since there are no bodies in the World to Come, it follows that there is neither eating, nor drinking, nor any of the things which human bodies require in this world. Neither do souls perform any bodily action such as sitting and standing, sleeping and dying, weeping or laughing. It is obvious that there is no corporeal existence in the world of Eternity since there is no eating and drinking.” 
Part of deciphering Maimonides’ theological thought depends on how one wishes to define his use of the term “soul” ? Upon a careful reading of Maimonides, one will find that he does not refer not to the soul, at least as it was conceived by the Aristotle or his followers, but rather refers to soul as the power of the reason, which facilitates a knowledge of the Divine (ibid., 8:3). Maimonides hedges between Aristotle and the Talmudic belief. In Maimonides’ schema of the soul, the only part of the human persona that endures beyond death, is the part of human intellect that acquires an awareness of metaphysical truths; if worthy, such an individual gains what Maimonides describes as an “acquired intellect” (sechel HaNikneh).
Elsewhere, in Maimonides’ elaborate parable of the palace, he boldly writes that the men who know physics and metaphysics together with the prophets (who are of course by definition philosophers) enter the castle while those who study the Law (i.e., the Talmudists?) are looking futilely for a way in. So scandalous was Maimonides’ parable, he created such a major uproar in rabbinic circle; consequently, many of his books were publicly burnt in many communities. One commentary to Maimonides’ Guide scathingly wrote:
“Many rabbinical scholars declare that the Master did not write this chapter, and if he did, it must be hidden, or more fittingly – burned. How could he have placed those who know natural things in a higher rank than those who occupy themselves with religion, and especially, how could he dare place them in the ‘inner court of the king? If this was so, then the philosophers who concern themselves with science and metaphysics rank above those who devote themselves to the Torah.” 
In short, Maimonides felt it necessary to be occasionally subtle; he knew that he could only have limited success in educating his generation because they were not ready to hear the truth as he understood it. In his Guide, Maimonides really expresses his most intimate thoughts; he carefully preserved his true ideology in his Guide and knew that someday future generations would become more receptive to the wisdom he wished to impart. Eventually, he knew that his radical ideas redefining the world of Jewish theology and belief would eventually be vindicated.
Notes: MT: Hilchot Teshuvah, 8:2.  Guide 3:5.