Jalaluddin Mohammad, a warrior, son of Emperor Humayun and Hameeda Bano Begum, became the Emperor of the Mughal dynasty at a very young age. He is under the influence of his regent Bairam Khan and his foster mother Maham Anga. Khan trains Jalal to be a ruthless ruler and control his kingdom through terror and fear. Jalal becomes heartless and fearsome but a fair and religious ruler whom the people dislike. He wants to conquer the entire Hindustaan and eyes the golden Rajputana. Jodha Bai, princess of Amer, daughter of Raja Bharmal and Rani Mainavati, is a kind and intelligent young girl who believes that rule is spread by love and togetherness, not by force.
When Jodha is at a temple to offer prayers on her birthday, along with Moti Bai, her friend, a band of mughal soldiers enter the temple to loot the jewellery on the goddess. When Moti tries to stop them, they try to molest her. Angered, Jodha pledges to destroy Jalal and present his head before the goddess. Later, Moti, embarrassed by the turn of events, decides to commit suicide, but Jodha prevents her.
Meanwhile, Jalal, with the help of Sujamal, attacks Amer and wins the battle. He demands high monthly taxes from Amer by keeping Jodha's brothers as hostage. Later, when Sharifuddin keeps increasing his demands, King Bharmal's friend suggests that he meet Jalal to negotiate. During the meeting, Bharmal's friend advises to marry Jodha to Jalal. Jodha disagrees and tries to poison herself but after much persuasion agrees to the marriage for Amer's safety, but with two conditions: to remain a Hindu after her marriage and carry the statue of Krishna with her to Agra. Jalal agrees despite the protests of his courtiers and advisors, as he wants to humiliate her in return of her insults. After the marriage, Jodha maintains her distance. Later, Jalal's favorite wife and childhood friend, Rukaiya, becomes pregnant. The kingdom rejoices at the thought of an heir, but the happiness is short-lived as Maham Anga poisons Rukaiya that leads to a miscarriage. Anga frames Jodha and her family for the miscarriage, but Jodha is proved innocent. Jalal accepts his mistake and feels guilty for doubting Jodha. He gives Jodha freedom to divorce him and head back to Amer if she wishes. Jodha accepts but her mother refuses. Jodha tries to commit suicide but Jalal saves her. Jalal develops sympathy for Jodha. He realizes how lonely she has become. He starts spending more time with her. Jodha realizes Jalal means well for his people.
Jalal and Jodha finally fall in love. Jodha becomes pregnant with twins, one of whom Rukaiya claims. While Jalal denies her claim, Jodha promises her one of the twins. The twins are killed shortly after birth, their death plotted by Jalal's enemies, who hunts them down and kills them. The death of the twins leaves the kingdom in sorrow and Jalal, Jodha and Rukaiya are devastated. Jodha and Jalal again grow distant while Jalal turns into his former cruel self to avenge his sons' lives. He stays away from his court in Salim's sanctuary, along with Jodha for two years and serves him with deep devotion. Jodha and Jalal reconcile, and Jodha becomes pregnant giving birth to another son whom Jalal names Salim. Jalal and Jodha return to court and upon seeing the child, Rukaiya tries to claim on him but is met by Jalal's wrath. She then vows to destroy Salim.
Salim, a few years older, is loved by everyone. He meets a girl Nadhira who is the daughter of the woman who once saved Salim's life when he was a baby by informing Jodha of the attack planned on them. Nadhira and Salim instantly dislike each other. Salim is being manipulated by Rukaiya through wine and drugs. She plants false scenarios in Salim's mind to make Salim hate his parents and entices him into women and addictions. His behaviour becomes more irrational which leads to the banishment of Nadhira and her family. This angers Jalal to the point that he sends Salim to live in a war field until he becomes an adult. Salim grows up to be indifferent, hating his parents but has a soft spot for Rukaiya. Upon returning to Agra, Salim bonds with his brothers but never seeks his parents. He falls in love with a girl, Anarkali, only to discover she is Nadhira. She had changed her name to find work in Agra. Salim hates her thinking he had been betrayed.
Salim and Anarkali work out their relationship facing problems because of the difference in their social status. Rukaiya's true intentions are unveiled. Salim realises his mistakes and regrets not trusting his parents more.
Unknown as Tejwant: an ordinary craftsman; Shivani's husband
Bobby Kumar as Atemat: a dancer (Kasim). He appeared in the episode of Sujamal's case about sending a letter to Jodha and he also witnessed with his own eyes that Atgah Khan was killed by Adham Khan. (2013)
Certain Rajput groups claimed Jodhaa was married to Akbar's son, Jahangir, not Akbar, whereas certain reports state that Jodha and Akbar were not married, although the primary history proves that Akbar and the princess of Amber were married on which the show is made as a complete show can't be false. They also protested against the show along with Bharat Ka Veer Putra – Maharana Pratap, another historical series that aired on Sony TV.[8]
The title of the series was criticised by members of the Kshatriya community as misleading, politically motivated historical revisionism that minimised Rajput history. The community protested against the series in Rajasthan, and alleged that if the name was not changed, they would not let any Balaji Telefilms films to be released in the state.[8] Ekta Kapoor stated, "I always believe it's 80% history and 20% folklore. There are enough proofs that say it's true, but then some people say it's not. Akbar had a certain graph and we know that. We cannot negate that he changed his heart from a power-hungry ruler to a non-biased one because of his Rajput queen."[9]