‘Main Krishna Hoon’ is about an orphan boy, who longs to have his own parents someday, finds happiness when he befriends Lord Krishna. Kantaben (Juhi Chawla) runs an orphanage and funds it by mostly running a small-scale pappad business.

One rainy night, she finds a baby abandoned in a basket, outside her orphanage. The baby is rescued from floodwaters by Kantaben. She takes him in and nurtures him. The circumstances in which she finds the baby, reminds her of Lord Krishna's birth and childhood. She thus names the boy (Namit Shah) Krishna. Orphan Krishna lives happily in the orphanage with Kanta and the other foundling children.

But over the years, as one by one his other friends are adopted out to families but he remains, young Krishna comes to believe that he is unadoptable, unwanted, and will never find a family. Krishna suffers from epilepsy. In despair, all alone one night he goes to a temple and prays to Lord Krishna.

This is the story of how Lord Krishna himself (in his mischievous childhood makhan chor 'butter thief' avatar) comes to Earth and befriends the young orphan Krishna. Many adventures then ensue, as Krishna-from-Heaven helps Krishna-from-Earth to discover his family.