Heidi, an orphan girl since she was 1 year old, has grown up under the care of her aunt Dete. However, just as she turns 5, Heidi is sent to live with her formidable grandfather Onji in the Swiss Alps when her aunt gets a housemaid job in Frankfurt. Heidi soon befriends a goatherd named Peter, and she is amazed with the beauty of the natural surroundings and explores her new home with visible satisfaction as Onji gets lost in his thoughts.

Heidi enjoys the simplicity and the freedom of her new life. Having been forced to seclusion before, she enjoys running around playing with the goats and enjoying the pleasures of nature. She makes herself a hay bed and explores her new home, while her grandfather Onji is won over bit by bit by her laughter, intelligence and enthusiasm.

After spending her first night at her grandfather's house, Heidi wakes up to the happy realization that her newly-acquired happiness is not a dream. Onji allows Heidi to join Peter on his trip to the meadow. The routine of the young goatherd becomes an adventure for the little girl. She learns a couple of valuable lessons and comes back home excited to share them with Onji.

Day after day, Onji realizes with great pleasure that Heidi is adapting fine to the hard life in the Alms mountains. While Heidi is at the high pastures with Peter, a storm surprises them and force the kids to take refuge for a while. Once the storm has passed, Heidi finds a little bird that has fallen from the nest, names him Picchi and takes him under her care. Peter is jealous because the girl refuses to go to the pastures with him the next day to take better care of the bird.

Peter is entrusted with delivering a letter to Onji. Heidi distracts him showing the kid how Picchi has already learnt to fly and they leave to the high pastures where some goats get lost as the kids play. Peter and Heidi find the goats but a thick fog isolates them. Joseph, Ohi's dog, finds them and shows them the way back to the pastures where Onji waits. At the end of the day, he gets to read the letter that brings news from her aunt, who is well and happily established, wishing for Heidi to join her. Onji throws the letter to the fire. He can't conceive his life without the little girl now.

The Delphi kids are jealous of Peter's preference for Heidi. Onji comes down from the mountains to sell the wooden utensils he crafts and the cheese he makes to get groceries and all he needs in return. Convinced that the Delphi baker has tried to cheat him, Onji leaves angry and heads to a further village, where he gets a good deal. At his return, he finds Heidi home who is excited with all the things she's learnt during the day: now she can milk and whistle like a good goatherd. Onji observes her proudly and treats her with a yummy sweet he's bought for her.

Heidi has been living in the mountains for 3 months already, and the summer is coming to an end. The weather is not that pleasant anymore, so Onji decides that it's not safe for Heidi to join Peter in the meadows any more and the girl stays at home from now on. She learns how to make cheese and also that life in the mountain has a tough side full of work, responsibility and discipline.

Heidi is confronted with the hard reality of Picchi migrating with its kind. Moreover, she gets angry at Peter because the boy thinks that Picchi has left because the bird doesn't love her anymore. Onji calms her down, takes her for a walk and explains to the girl that Picchi needs a warmer place to spend the winter. Peter catches a bird for Heidi to make up with her. The kids become friends again but Heidi decides to free the bird so it can migrate too and isn't left behind alone.

The winter is around the corner and the first snowfall fills Heidi with joy. However, that means that Peter and the goats won't go back to the meadows until Spring, and Heidi gets isolated at home. It wouldn't take long for her to make new friends though. On Sunday, Peter visits Heidi and lets her know that his grandmother has invited her to visit. Onji is not happy with the idea.

Heidi wakes up earlier than usual; she is excited to go visit Peter's grandmother. However, the weather delays the visit for some days. When Heidi finally visits Peter's house, she is discouraged about the ruined look of it, and she gets further distraught when she find out that the granny is blind. After spending a nice afternoon, she leaves with the promise of a soon return. One day afterwards, Heidi is back with a surprise.

The winter in the mountain is long and severe. Heidi visits Peter's grandmother when the weather allows for it, but one clear day, Ohi foresees a snowstorm coming in. As she is feeding the animals that come for shelter under the nearby fir trees, Heidi gets in the way of some hunters and saves a fawn's life. The hunters insist on going on towards the mountain tops despite Heidi's advice to the contrary. As predicted, the storm hits hard and finally, due to the girl's concern, Ohi decides to go out and save the men's lives.

The signs of an approaching spring are everywhere. While Heidi is playing with Joseph, she notices that the firs are shaking off the snow and beginning to sound in the wind, primroses start to show over the snow and avalanches sound in the distance. While riding a sledge, two kids from Delfli challenge Heidi and Peter to a race. Rain catches them on their way back home and makes the snow melt faster. Ohi comes to their encounter and saves the kids from an avalanche in the last minute. Spring has arrived to the mountain.

With the arrival of the spring, Peter's job as a goatherd starts again. He gathers all the goats and goes back to the meadows in Heidi's company. The mountain is full of activity again: the animals are busy everywhere, the birds are back and the fields are filled with flowers. A storm makes them seek for refuge, where a lost goat joins their flock. Its owner, a bad tempered shepherd, accuses them of thieves and gets into a fist fight with Peter. Joseph comes to the kids' rescue.

Peter is the bearer of bad news when he learns that Heidi's favourite goat is going to be sacrificed after the summer because it doesn't provide with enough milk. Heidi gets devastated by the news and her grandfather's words won't put her at ease. After having a nightmare at night, Ohi advices her to feed the goat with a particular kind of herb that could save the animal's life. Peter and Heidi spend the whole summer doing so.

The summer is almost gone and the owners of Heidi's favourite goat decide not to send it anymore to the meadows to be sacrificed. It's a bittersweet day for Heidi and Pedro, who have fun in their last day with the goat but at the same time see their summer efforts unfruitful. In the very last moment, Heidi hides the goat at her grandfather's putting Peter's job at a stake, so the boy confesses where it is. When its righteous owner shows up to claim what is his own, Heidi manages to convince him to let the goat live.

Heidi, Onji, Josef and Chi return to the mountain hut for the summer, bidding farewell to the village of Delifi. Meanwhile, Clara reminds her father of his promise to let her visit Heidi in the Alps.