When she grows up, Amélie becomes a waitress in a small Montmartre café, The Two Windmills, run by a former circus performer. The café is staffed and frequented by a gang of eccentrics. By age 22, life for Amélie is simple; having spurned romantic relationships following a few failed efforts, she has devoted herself to simple pleasures, such as cracking crème brûlée with a teaspoon, going for walks in the Paris sunshine, skipping stones across St. Martin's Canal, trying to guess how many couples in Paris are having an orgasm at one moment ("Fifteen!", she informs the camera), and letting her imagination roam free.

Her life changes on the same day that Princess Diana dies. Following a series of circumstances resulting from her shock at the news, behind a loose bathroom tile she finds an old metal box of childhood memorabilia hidden by a boy who lived in her apartment decades ago. Fascinated by the find, she resolves to track down the now grown-up man who put it there and return it to him, making a deal with herself in the process: if she finds him and it makes him happy, she will devote her life to goodness. If not, too bad.

She meets her reclusive neighbor Raymond Dufayel, a painter who continually repaints Luncheon of the Boating Party (Le Déjeuner des canotiers) by Pierre-Auguste Renoir. He is known as 'the Glass Man' because of his brittle bone condition. With his help, she tracks the former occupant down, and places the box in a phone booth, ringing the number as he passes to lure him there. Upon opening the box, the man has an epiphany as long-forgotten childhood memories come flooding back. She trails him to a nearby bar and observes him secretly. On seeing the positive effect she had on him, she resolves from that moment on to do good in the lives of others. Amélie becomes something of a secret matchmaker and guardian angel, as she persuades her father to follow his dream of touring the world (with help from his garden gnome and an air-hostess friend), her co-workers and friends (two of whom she sets up), the concierge of her building, and Lucien, the boy who works for the bullying owner of the neighborhood vegetable stand (Mr. Collignon, upon whom Amélie delights in playing pranks).

However, while she is looking after others, no one is looking after Amélie. In helping other people achieve happiness, she is forced to examine her own lonely life - made ever more apparent and painful by her relationship with Nino Quincampoix, a quirky young man who collects the discarded photographs of strangers from passport photo booths, with whom she has fallen in love. Although she intrigues him through her various roundabout methods of attraction (including something like a treasure hunt for one of his forgotten photo albums), she is painfully shy and incapable of actually approaching him. It will take Raymond's friendship to teach her to pursue her own happiness whilst still ensuring that of her friends and neighbours.