Pepper is raising interest rates for some of the variable mortgage rate customers, by between 0.5% and 1%.
The increase will impact approximately 9,450 customers, and will take affect from next month.
The move will bring Pepper's average variable mortgage rate from 5.9% to 6.3%.
However - as the company services mortgages for a large number of providers - there are considerably different rates charged across its variable mortgage accounts.
That means that many customers may be paying a higher rate, while others' rates will be below that.
Pepper last raised its variable interest rates in February, however it said three separate European Central Bank rate increases have been announced since then.
Variable customers affected by the move are due to receive letters from Pepper this week, giving them 30 days notice of the change.
The company urged those struggling to meet their repayments to engage with them in order to find a solution.
It said it had also been actively reaching out to customers on higher rates to assess their ability to meet their monthly repayments.
While thousands of Pepper's variable mortgage rate customers will not see their rate increase as part of this move, they may face changes at another time.
The European Central Bank is due to meet again on Thursday, with another 0.25% increase in its main lending rate widely anticipated.
