Mullin wore boots with a slogan about the Conservative Party.
Mullin revealed the custom-made boots on social media.
The photographs were taken without the knowledge or approval of the owners of the company.
The club takes a neutral stance on politics.
The issue will be dealt with quietly.
Mullin's social media post was described as an "unwelcome distraction" by the club in a statement.
The club can confirm that the boots revealed by Paul Mullin on social media will not be worn in tonight's game, and that the photographs taken at the Racecourse Ground were done without our knowledge or approval.
Had we known, the pictures wouldn't have been allowed to be taken, and the issue will be dealt with by the club.
The club has adopted a neutral position on many matters with a political aspect.
The club acknowledges that everyone is entitled to their own opinion, whether that be employees or supporters, but also highlights that an individual view cannot be fairly attributed, as the view of everyone or the club itself.
There is no more prominent example of this than the fact that the Member of Parliament for the constituency in which the club is located is a Conservative.
The club hopes the focus stays on our objectives of gaining promotion on the field and creating community benefit off it, in which Paul Mullin will continue to play a significant part.
Mullin was the most eye-catching signing so far when he joined Cambridge United.
The National League player of the year last season, the forward has scored 11 goals in 14 appearances this season.