As told in the Qur'an: Prophet Yusuf was the only holy man among his 12 brothers. They lived in Canaan (modern day southern Levant). At a young age he fell victim to the jealous trickery of his brothers, who coerced him into climbing down a well to bring up water with the promise of pulling him out. They left him in the well to die. He was discovered by men who were in the slave trade. Subsequently, he was rescued, taken to Egypt, and sold into service for a high-level servant to the Pharoah and his wife. Due to his captivating beauty and admirable candor, Yusuf rose in the ranks in their palace but attracted jealousy and anger from the Egyptian idolater ministers who rejected his Muslim faith. Yusuf's faith is put to the test throughout the story as the Pharoah's wife, characterized by the story as the evil (Sheytaani / شیطانی) manifestation of the sin of temptation (Havvas / هوس), attempts to initiate a romantic and sexual relationship with him.

The Qur'anic story goes further in content, but the manuscript predominantly focuses on the relationship between Yusuf and Zoleikha and on bifolio 42, the poet Jami praises this story over other Persian romance epics, including Leili o Majnoon (لیلی و مجنون) and Khosrow o Shirin (خسرو و شیرین):

دهم از دل برون راز نهان را / I will let this secret out of my heart

بخندانم بگریانم جهان را / I will make the world laugh and cry

کهن شد دولت شیرین و خسرو / The story of Shirin and Khosrow is old

به شیرینی نشانم خسرو نو / I will create a new Khosrow

سرآمد نوبت لیلی و مجنون / Leili and Majnoon's turn are over

کسی دیگر سرآمد سازم اکنون / Now I shall make another the leader ["Leader" here has been translated directly from the Farsi word Sardaar / سردار but in this context it means hero or protagonist, alluding to Yusuf]

چو طوطی طبع را سازم شکرخا / And I will satisfy the heart's desire for sweetness (like a parrot desires sugar)

ز حسن یوسف و عشق زلیخا / By telling the tale of Yusuf and Zoleikha

Although the manuscript is not divided into chapters, several brief, illuminated descriptors appear throughout. These serve the purpose of summarizing that section of the story. They have been written in red ink, distinctive from the ink used elsewhere in the manuscript.

Some of the illustrations appear to belong together as groupings, or are continuations of the same narrative. Illustrations associated with folios 102, 107, 109, and 111, for example, depict Zoleikha at the peak of desperation in her desire to be with Yusuf. She invites him into her chamber, which is locked behind seven doors. During their conversation, Yusuf pleads for her to refrain from such impure behavior and let him go. She refuses and he decides to make his escape through the seven doors that were previously locked. He calls to Allah for help and thus the doors unlock as he passes through them. When Yusuf reaches the seventh door, Zoleikha catches up to him and reaches for him from the back, ripping his shirt. Potiphar catches them at the final door and when he asks about what has happened, Zoleikha blames Yusuf for indecent advances towards her. Yusuf denies this. At this time, Zoleikha's niece, who is an infant, speaks for the first time and says, "if the shirt is ripped from the back, Zoleikha is lying and if the shirt is ripped from the front, Yusuf lies."

In Jami's story, we are given a glimpse into Zoleikha's past as a single woman. Illustrations on folios 116, 117, 168 show her storyline. As a young girl, Zoleikha dreamt of a beautiful man and wanted to marry him. Her father informed her that he had found the man she was looking for and he lived in Egypt. Zoleikha became extremely excited and, after her father provided her with a grandiose dowry and an army of male and female servants who are all described to be beautiful, she moved to Egypt to marry her dream man. However, upon arriving in Egypt she realized to her disappointment that the man her father had told her about was not the man of her dreams, but was instead Potiphar.

Eventually, Potiphar decided to trust his wife and imprison Yusuf for wrongdoing. While in prison, Yusuf's interpretations of dreams amazed his fellow prisoners, and they became believers in his divinity. The outside world also missed Yusuf, for he had been the kindest man to all staff at Potiphar's palace, so much so that the servants who worked for Zoleikha confessed that she had lied about Yusuf's advances and demanded the release of their innocent friend. Potiphar himself had liked Yusuf, and the confessions of others became confirmation that his wife was an adulterer and a conspirator. He called for Yusuf's release after a few years.

Bifolio 13, right side

Zoleilkha, before her marriage to Potiphar, famously dreams of Yusuf before knowing of his existence. In this illustration, Zoleikha lies with her head in the lap of an apparition of Yusuf. Three servants are keeping watch over her, although they are all asleep while sitting up

Bifolio 15, left side

This illustration shows the immediate aftermath of Zoleikha's dream. She is in her garden with servants at her feet and around her. They stand concerned for she has been driven insane by love and is eager to find the man she saw in her dream: Yusuf

Bifolio 41, right side

One of the smaller illustrations in the manuscript. Yusuf and Zoleikha are seated and conversing, two pieces of bread in front of them. They are surrounded by four servants who fan them and bring them more bread

Bifolio 52, right side

This illustration shows Zoleikha seated on her gilded chair surrounded by 11 servants who fan her and bring her bread

Bifolio 54, right side

Zoleikha sees Yusuf in her dream

Bifolio 63, right side

Zoleikha spots Yusuf in a field and recognizes him as the man in her dreams. She stops to ask him who he is

Bifolio 63, left side

Zoleikha kneels at Yusuf's feet and expresses her love for him

Bifolio 72, right side

Yusuf tells Zoleikha the story of his life and how his brothers tricked him into a well and left him to die. Zoleikha and her servant weep upon hearing this

Bifolio 89, right side

The servants at Potiphar and Zoleikha's palace surround Yusuf in fascination and converse with him

Bifolio 102, left side

Yusuf is present in Zoleikha's chambers at her request

Bifolio 107, right side

Continuation of 102. Zoleikha has become aggressive in her attempt to persuade Yusuf to elope, and he is trying to calm her

Bifolio 109, right side

Yusuf attempts to run away from Zoleikha's chambers by passing through the seven doors. Zoleikha reaches for the back of his shirt

Bifolio 111, right side

Potiphar catches the couple at the seventh door

Bifolio 115, right side

Egyptian women cut their wrists as Yusuf enter the room

Bifolio 116, right side

Zoleikha rides into Egypt and the people who are unaware of her unhappiness and overjoyed for the new bride, greet her by throwing jewels at her feet

Bifolio 117, right side

Zoleikha is seated in the palace of Potiphar and servants adorn her with gifts. She is in a deep depression

Bifolio 121, left side

An Angel visits Yusuf's father, Yaqub, and his brothers and tells them that Yusuf is alive

Bifolio 126, right side

Zoleikha is informed of the location of her beloved and rides there with her servants

Bifolio 132, right side

Egyptian idolater ministers and Potiphar are amazed by the grace of Yusuf, and bow to him. Yusuf has now completely embraced prophethood

Bifolio 141, right side

Yusuf's brothers meet to think about ways to keep Yusuf away from their father

Bifolio 145, right side

Yusuf's brothers lure him away from their father in front of his eyes and take him with them on their trip to the desert

Bifolio 145, left side

Once in the desert, Yusuf's brothers strip him and take his shoes

Bifolio 148, left side

Yusuf's brothers have thrown him into the well

Bifolio 149, left side

An angel visits Yusuf in the well and tells him he is a prophet of God ["God" and "Allah" are used interchangeably] and assures him that he will come out of the well safely

Bifolio 151, left side

Egyptian slave traders find Yusuf in the well and rescue him. They then enslave him

Bifolio 152, left side

Upon arriving in Egypt with the slave traders, Yusuf washes himself in the Nile. The people around him, among them the staff at Potiphar's palace, are stunned by his beauty

Bifolio 168, left side

Zoleikha's beautiful army of male and female servants are depicted

Bifolio 192, right side

Yusuf meets with Potiphar after his release

Bifolio 194, right side

Zoleikha's infant niece speaks for the first time to serve as witness to Yusuf's innocence and Zoleikha's lie