Blaming regulation and increased demand, the investment firm wrote to customers over the festive period to tell them that quarterly charges for its Individual Savings Account (ISA), and investment dealing account would rise from £12 a quarter to £22.50, including value added tax.
This means that from February 1 investors face paying £90 a year, on top of dealing charges, up from £48 currently. Charges have tripled in 18 months. ATS had a £30 a year fee on its ISA until August 2012.
ATS, which had £4.7 billion in assets under administration as of the end of June, is owned by investment company Alliance Trust, whose chief executive Katherine Garrett-Cox was given a CBE in the New Year honours list.
Investors use ATS accounts to trade shares in Alliance Trust and other investment companies, as well as funds and UK and overseas stocks.
An ATS spokesman said: "What we can confirm is we are reviewing the current prices. They (Alliance Trust Savings) obviously remain very committed to being transparent and operating a flat fee charging model."
Justin Modray, founder of CandidMoney.com, said: "While it is disappointing to see Alliance Trust Savings raise its annual account charge fees, in fairness they remain very competitive for investors with portfolios of around £50,000 or more who don't trade frequently."
In a letter to investors, ATS managing director Patrick Mill said the changes had been made in response to customer feedback and "increased demand on our business".
Some transactions such as cash withdrawals will no longer have fees levied on them.
Mr Mill said: "We realise that an increase in price will not be popular but it is necessary to help us maintain the standard and quality of our service to customers and ensure we are meeting the increasing regulatory standards that are being placed on platform providers."
Investors in ATS's self-invested personal pension will see their annual charges rise to £186 from £162.
Charges for children's accounts have been frozen at £12 a quarter, which ATS said meant it was subsidising the accounts.
Investors holding just Alliance Trust shares can switch to a lower-cost account.
ATS said it would not increase its charges again until 2016 at the earliest.
ATS was established in 1986 but has struggled to make a profit and has been overhauled since Ms Garrett-Cox became Alliance Trust chief executive in 2008.