The charges, initially considered a legitimate expense by the Scottish Parliament, were due to an outdated sim card. Matheson, earning a yearly salary of £118,511 and having already paid £3,000 towards the bill, faced scrutiny after it was revealed he had been previously warned about the sim card issue.
The decision to cover the costs comes amid criticism from opposition MSPs and questions about First Minister Humza Yousaf's initial defense of the expenses as legitimate.
The controversy has led to a review of mobile data usage policies in the Scottish Parliament and the implementation of a new mobile phone contract to avoid similar incidents.
Matheson's decision to repay the bill, which exceeds the total phone-related expenses of all MSPs from the previous year, is seen as a move to maintain his ministerial position and personal integrity.