The investment and savings platform will charge £75 annually before VAT for Isa and investment dealing accounts.
For a select Sipp the fee is rising from £135 to £155, plus VAT, with all changes taking effect on 1 February.
ATS said it is committed to keep charges at the new level until at least 2016.
Patrick Mill, managing director at Alliance Trust Savings, said the move was necessary to maintain high standards and the quality of service.
He said: "We remain fundamentally committed to a transparent flat fee model as the value of an individual account does not change the cost of administering it.
"We believe percentage charging structures are simply a tax on wealth.
"However, we have listened to feedback from our customers about the service we provide, our online service and the ad hoc charges that we apply to their accounts.
"Based on this feedback and the increased demand on our business, we have decided to move to a single, all-in-one administration fee which covers all regular activities customers carry out on their accounts."
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Online and offline dealing fees remain unchanged and fees on child accounts have been frozen.
ATS is offering free transfers until 28 February to customers who decide to move their investments.
Also, for all online trades, a loyalty discount is being introduced, with the highest being for customers of over 20 years who will get 25% off.