The three-year-old was filmed leaving the service at The Chapel Royal, St James' Palace with her family on Monday.
The monarch, 92, has a busy week ahead, with high-profile celebrations in central London marking the centenary of the RAF on Tuesday, and a visit by US President Donald Trump in Windsor on Friday.
The gesture comes nearly two months after the princess gave a little wave to the world on the steps of St George's Chapel at the royal wedding in May. As after George and Charlotte's baptisms, guests will be served slices of the duke and duchess's wedding cake.
Louis was carried into the chapel by his beaming mother, wearing the handmade replica of the royal christening robe, which in 2008 replaced the original that had been worn for all royal christenings since that of Queen Victoria's eldest daughter in 1841.
According to Kensington Palace, the couple named several of their closest friends along with a few distant relatives as the prince's godparents including Mr. Nicholas van Cutsem, Mr. Guy Pelly, Mr. Harry Aubrey-Fletcher, The Lady Laura Meade, Mrs. Robert Carter, and Miss Lucy Middleton.
Royal babies are baptised in the same intricate cream lace christening gown.
The whole family stepped out for Louis's special day, and their royal fashion prompted plenty of comments on Yahoo Entertainment.
From the duchess's side, Kate's parents Michael and Carole, brother James, pregnant sister Pippa and her husband James Matthews were there.
The Duke of Sussex reportedly purchased a first edition copy of "Winnie-the-Pooh" by AA Milne for his youngest nephew. Duchess of Cambridge Kate Middleton wore a white structured Alexander McQueen dress with a Jane Taylor headpiece.