Jacopo Carucci was born at Pontorme, near Empoli, to Bartolomeo di Jacopo di Martino Carrucci and Alessandra di Pasquale di Zanobi. Vasari relates how the orphaned boy, "young, melancholy and lonely," was shuttled around as a young apprentice:

Jacopo had not been many months in Florence before Bernardo Vettori sent him to stay with Leonardo da Vinci, and then with Mariotto Albertinelli, Piero di Cosimo, and finally, in 1512, with Andrea del Sarto, with whom he did not remain long, for after he had done the cartoons for the arch of the Servites, it does not seem that Andrea bore him any good will, whatever the cause may have been.

Pontormo painted in and around Florence, often supported by Medici patronage. A foray to Rome, largely to see Michelangelo's work, influenced his later style. Haunted faces and elongated bodies are characteristic of his work. An example of Pontormo's early style is The Visitation of the Virgin and St Elizabeth, with its dancelike, balanced figures, painted from 1514 to 1516.

This early Visitation makes an interesting comparison with his painting of the same subject, which was done about a decade later for the parish church of St. Michael in Carmignano, a few miles from Florence. Placing these two pictures together — one from his early style, and another from his mature period — throws Pontormo's artistic development into sharp relief. In the earlier work, Pontormo is much closer in style to his teacher, Andrea del Sarto, and to the early sixteenth century renaissance artistic principles. For example, the figures stand at just under half the height of the overall picture, and though a bit more crowded than true high renaissance balance would prefer, at least are placed in a classicizing architectural setting at a comfortable distance from the viewer. In the later work, the viewer is brought almost uncomfortably close to the Virgin and St. Elizabeth, who drift toward each other in clouds of drapery. Moreover, the clear architectural setting that is carefully constructed in earlier piece has been completely abandoned in favor of a peculiar nondescript urban setting.

The Joseph canvases (now in the National Gallery in London) offer another example of Pontormo's developing style. Done around the same time as the earlier Visitation, these works (such as Joseph in Egypt) show a much more mannerist leaning. According to Giorgio Vasari, the sitter for the boy seated on a step is his young apprentice, Bronzino.

In the years between the SS Annunziata and San Michele Visitations, Pontormo took part in the fresco decoration of the salon of the Medici country villa at Poggio a Caiano (1519 – 20), not far from Florence. There he painted frescoes in a pastoral genre style, very uncommon for Florentine painters; their subject was the obscure classical myth of Vertumnus and Pomona in a lunette.

In 1522, when the plague broke out in Florence, Pontormo left for the Certosa di Galluzzo, a cloistered Carthusian monastery where the monks followed vows of silence. He painted a series of frescoes, now quite damaged, on the passion and resurrection of Christ.

The large altarpiece canvas for the Brunelleschi designed Capponi Chapel in the church of Santa Felicita in Florence, portraying The Deposition from the Cross, is considered by many Pontormo's surviving masterpiece (1528). The figures, with their sharply modeled forms and brilliant colors are united in an enormously complex, swirling ovular composition, housed by a shallow, somewhat flattened space. Although commonly known as The Deposition from the Cross, there is no actual cross in the picture. The scene might more properly be called a Lamentation or Bearing the Body of Christ. Those who are lowering (or supporting) Christ appear as anguished as the mourners. Though they are bearing the weight of a full-grown man, they barely seem to be touching the ground; the lower figure in particular balances delicately and implausibly on his front two toes. These two boys have sometimes been interpreted as Angels, carrying Christ in his journey to Heaven. In this case, the subject of the picture would be more akin to an Entombment, though the lack of any discernible tomb disrupts that theory, just as the lack of cross poses a problem for the Deposition interpretation. Finally, it has also been noted that the positions of Christ and the Virgin seem to echo those of Michelangelo's Pietà in Rome, though here in the Deposition mother and son have been separated. Thus in addition to elements of a Lamentation and Entombment, this picture carries hints of a Pietà. It has been speculated that the bearded figure in the background at the far right is a self-portrait of Pontormo as Joseph of Arimathea. Another unique feature of this particular Deposition is the empty space occupying the central pictorial plane as all the Biblical personages seem to fall back from this point. It has been suggested that this emptiness may be a physical representation of the Virgin Mary's emotional emptiness at the prospect of losing her son.

On the wall to the right of the Deposition, Pontormo frescoed an Annunciation scene. As with the Deposition, the artist's primary attention is on the figures themselves rather than their setting. Placed against white walls, the Angel Gabriel and Virgin Mary are presented in an environment that is so simplified as to almost seem stark. The fictive architectural details above each of them, are painted to resemble the gray stone pietra serena that adorns the interior of Santa Felicità, thus uniting their painted space with the viewer's actual space. The startling contrast between the figures and ground makes their brilliant garments almost seem to glow in the light of the window between them, against the stripped down background, as if the couple miraculously appeared in an extension of the chapel wall. The Annunciation resembles his above mentioned Visitation in the church of San Michele at Carmignano in both the style and swaying postures.

Vasari tells us that the cupola was originally painted with God the Father and Four Patriarchs. The decoration in the dome of the chapel is now lost, but four roundels with the Evangelists still adorn the pendentives, worked on by both Pontormo and his chief pupil Agnolo Bronzino. The two artists collaborated so intimately, that specialists dispute which roundels each of them painted.

This tumultuous oval of figures took three years for Pontormo to complete. According to Vasari, because Pontormo desired above all to "do things his own way without being bothered by anyone," the artist screened off the chapel so as to prevent interfering opinions. Vasari continues, "And so, having painted it in his own way without any of his friends being able to point anything out to him, it was finally uncovered and seen with astonishment by all of Florence..."

A number of Pontormo's other works have also remained in Florence; the Uffizi Gallery holds his mystical Supper at Emmaus as well as portraits.

Many of Pontormo's well known canvases, such as the early Joseph in Egypt series (c. 1515) and the later Martyrdom of St Maurice and the Theban Legion (c. 1531) depict crowds milling about in extreme contrapposto of greatly varied positions.

His portraits, acutely characterized, show similarly Mannerist proportions.

Many of Pontormo's works have been damaged, including the lunnettes for the cloister in the Carthusian monastery of Galluzo. They are now displayed indoors, although in their damaged state.

Perhaps most tragic is the loss of the unfinished frescoes for the church of San Lorenzo which consumed the last decade of his life. His frescoes depicted a last judgement day composed of an unsettling morass of writhing figures. The remaining drawings, showing a bizarre and mystical ribboning of bodies, had an almost hallucinatory effect. Florentine figure painting had mainly stressed linear and sculptural figures. For example, the Christ in Michelangelo's Last Judgment in the Sistine Chapel is a massive painted block, stern in his wrath; by contrast, Pontormo's Jesus in the Last Judgment twists sinuously, as if rippling through the heavens in the dance of ultimate finality. Angels swirl about him in even more serpentine poses. If Pontormo's work from the 1520s seemed to float in a world little touched by gravitational force, the Last Judgment figures seem to have escaped it altogether and fly through a rarefied air.

In his Last Judgment Pontormo went against pictorial and theological tradition by placing God the Father at the feet of Christ, instead of above him, an idea Vasari found deeply disturbing:

But I have never been able to understand the significance of this scene, although I know that Jacopo had wit enough for himself, and also associated with learned and lettered persons; I mean, what he could have intended to signify in that part where there is Christ on high, raising the dead, and below His feet is God the Father, who is creating Adam and Eve. Besides this, in one of the corners, where are the four Evangelists, nude, with books in their hands, it does not seem to me that in a single place did he give a thought to any order of composition, or measurement, or time, or variety in the heads, or diversity in the flesh colours, or, in a word, to any rule, proportion or law of perspective, for the whole work is full of nude figures with an order, design, invention, composition, colouring, and painting contrived after his own fashion, and with such melancholy and so little satisfaction for him who beholds the work, that I am determined, since I myself do not understand it, although I am a painter, to leave all who may see it to form their own judgement, for the reason that I believe that I would drive myself mad with it, and would bury myself alive, even as it appears to me that Jacopo in the period of eleven years that he spent upon it sought to bury himself and all who might see the painting, among all those extraordinary figures... Wherefore it appears that in this work he paid no attention to anything save certain parts, and of the other more important parts he took no account whatever. In a word, whereas he had thought in the work to surpass all the paintings in the world of art, he failed by a great measure to equal his own (past) works; whence it is evident that he who seeks to strive beyond his strength and, as it were, to force nature, ruins the good qualities with which he may have been liberally endowed by her.

Vasari's Life of Pontormo, depicts him as withdrawn and steeped in neurosis while at the center of the artists and patrons of his lifetime. This image of Pontormo has tended to color the popular conception of the artist, as seen in the film of Giovanni Fago, Pontormo, a heretical love. Fago portrays Pontormo as mired in a lonely and ultimately paranoid dedication to his final Last Judgment project, which he often kept shielded from onlookers. Yet as the art historian Elizabeth Pilliod has pointed out, Vasari was in fierce competition with the Pontormo / Bronzino workshop at the time when he was writing his Lives of the Most Excellent Painters, Sculptors, and Architects. This professional rivalry between the two bottegas could well have provided Vasari with ample motivation for running down the artistic lineage of his opponent for Medici patronage.

Perhaps as a result of Vasari's derision, or perhaps because of the vagaries of aesthetic taste, Potormo's work was quite out of fashion for several centuries. The fact that so much of his work has been lost or severely damaged is testament to this neglect, though he has received renewed attention by contemporary art historians. Indeed, between 1989 and 2002, Pontormo's Portrait of a Halberdier, held the title of the world's most expensive painting by an Old Master.

Regardless as to the veracity of Vasari's account, it is certainly true that Pontormo's artistic idiosyncrasies produced a style that few were able (or willing) to imitate, with the exception of his closest pupil Bronzino. Bronzino's early work is so close to that of his teacher, that the authorship of several paintings from the 1520s and '30s are still under dispute — for example the four tondi containing the evangelists in the Capponi Chapel, and the Portrait of a Lady in Red now in Frankfurt.

Pontormo shares some of the mannerism of Rosso Fiorentino and of Parmigianino. In some ways he anticipated the Baroque as well as the tensions of El Greco. His eccentricities also resulted in an original sense of composition. At best, his compositions are cohesive. The figures in the Deposition, for example, appear to sustain each other: removal of any one of them would cause the edifice to collapse. In other works, as in the Joseph canvases, the crowding makes for a confusing pictorial melee. It is in the later drawings that we see a graceful fusion of bodies in a composition which includes the oval frame of Jesus in the Last Judgement.