If this is a security / privacy related question, there is nothing to stop a program running under Windows from reading the data
There is also nothing to prevent anyone to just run some live Linux from USB, so consider data on that Linux partition neither secure, nor private
I would say think twice whether you really need it. Encryption is another technological layer that can fail, so it is double edged sword and encrypting something “just to be on the safe side” might not be the best thing to do.