The annual report for the Dundee-based trust showed that Ms Garrett-Cox's base salary in 2013 remained unchanged at £425,000, her pension contributions were static at £106,000 and her taxable benefits also flat at £43,000.
But her annual bonus fell from £529,000 to £369,000 while the value of long-term awards dipped from £703,000 to £436,000.
The annual bonus payment in 2013 was 57.5% of what Ms Garrett-Cox could have received.
That was in spite of Alliance Trust increasing its dividend for the 47th consecutive year.
While its net asset value return of 18.4% for 2013 was its best for three years that performance also saw it fall into the third quartile of global investment trusts.
The total share price return in the year of 22.7% gave it a median ranking within its peer group.
The annual report states Ms Garrett-Cox, who also received a fee of euros 66,000 in 2013 for her role on the supervisory board at Deutsche Bank, will receive a 2.3% increase in her basic pay from April 1 this year, compared to an average 3% hike for other employees.
Finance director Alan Trotter saw his total package for 2013 reduce from £919,000 to £637,000 as a result of lower bonus and benefit allocations.
The number of senior and so-called code staff, whose actions can have a significant impact on the business, dropped from 27 to 22 in a year when several fund managers left.
Total fixed remuneration for those people came in at £3.6m in 2013, up from £3.5m.
Variable pay was down from £4.5m to £3.2m.
Alastair Kerr, chair of the Alliance Trust remuneration committee, said: "The driving principle behind our reward strategy is to link the delivery of strong performance closely to pay outcomes, thereby aligning the interests of directors and employees with those of shareholders and clients. The remuneration packages of executives will be structured in such a way as to promote sound and effective risk management within the company's risk appetite."
The report states that annual bonuses for executives for the 2014 financial year are capped at 150% of base salary. The remuneration committee said it is introducing clawback measures for bonuses for this year while also increasing the level of shareholding it requires executive directors to hold from 100% of salary to 150%.
Ms Garrett-Cox holds more than 550,000 shares at the moment and is line to receive close to a further 99,000 under a long term incentive plan which will vest in May this year.
The annual report states Alliance Trust chairman Karin Forseke received a fee of £120,000 for 2013.
The trust outlined in its annual report that the minimum Ms Garrett-Cox would receive for 2014 would be £565,856, her on-target remuneration would be more than £1.3m while the absolute maximum would be in excess of £3.45m.