Duchess Kate looked dreamy in a cream dress by Alexander McQueen as she arrived at the chapel and Princess Charlotte looked super cute in baby blue dress, with older brother Prince George wearing a white blouse and navy shorts.
Her Majesty, 92, is due to travel back from Norfolk Monday and has a busy week ahead with celebrations marking the centenary of the RAF on Tuesday, as well as Trump's visit to Windsor on Friday.
She will attend high profile celebrations in central London marking the centenary of the RAF on Tuesday, and a visit by USA president Donald Trump in Windsor on Friday.
However, the decision for them not to attend Louis' baptism at St. James's Palace in London was understood to have been mutually agreed by the sovereign and the Duke and Duchess of Cambridge some time ago, and was not health-related.
Kate's sister Pippa is expecting her first child.
Instead, the Duke and Duchess of Cambridge chose close friends and extended family members to be Louis' godparents.
The christening itself is quite the family tradition, Royal Central U.K. notes, adding Prince Louis also wore a replica of the now-famous Honiton lace christening gown.
It appears in photos that Middleton's other children, Prince George and Princess Charlotte, were not as relaxed as baby Louis at their own royal christenings.
Louis Arthur Charles weighed 8lb 7oz when he was born in the private Lindo Wing of St Mary's Hospital in Paddington, London, on 23 April.
Charlotte, who's fourth in line to the throne, is already excelling at being an older sibling.
Prince Louis had his royal christening on July 9, 2018.
The Cambridges have previously chosen close friends and confidantes for the role.
They include Guy Pelly, once dubbed the "court jester" to William and Harry for his wild ways that were often cited as a bad influence on the brothers in their youth, running their favourite drinking haunts.