However, according to the BBC, this was a decision made "some time ago" and it's not due to health reasons.
Prince Louis was sleeping as he arrived at the ceremony, held by his mother.
Her brother Prince George was holding their father's other hand, with Kate carrying a sleeping Prince Louis.
St Mary Magdalene was also where Charlotte's late grandmother, Diana, Princess of Wales, was christened on August 30, 1961.
Joining Mr Pelly as Prince Louis' godparents will be Nicholas van Cutsem, Harry Aubrey-Fletcher, The Lady Laura Meade, Sophie Carter and Lucy Middleton.
The godparents are all friends or family of William and Kate. Her hat was by Jane Taylor.
Kate's pregnant sister Pippa Middleton and her brother James Middleton were also at the ceremony.
The duchess added, with a smile: "I hope he stays like this".
The anthems were "This is the day which the Lord hath made" (John Rutter) and "Suo Gan, a traditional Welsh Lullaby" (Gareth Wilson).
They were joined by Prince Charles and the Duchess of Cornwall.
See how Prince Louis has grown!
At his christening on October 23, 2013 at the Chapel Royal at St. James's Palace in London, Prince George was dressed up in the newly made replica of the classic Victorian christening gown.
"This new version was commissioned by The Queen and made by Angela Kelly and her team as a copy of the famous original which was deemed too fragile to remain in use". As after George and Charlotte's baptisms, guests will be served slices of the duke and duchess's wedding cake. When Prince Louis was born she tickled everyone with her confident waving at cameras as she strolled up the steps of the Lindo Wing.
Charlotte, who's fourth in line to the throne, is already excelling at being an older sibling.