Microsoft claims that it is owed $6.9 million (£4.3 million) in unpaid interest from Samsung, as a result of the two firms' patent licence agreement.
Unsealed court documents revealed that Microsoft has accused the South Korean firm of refusing to pay interest on a late royalty payment of $1 billion (£625 million).
Samsung has since countered that Microsoft's 2013 acquisition of Nokia had already breached the terms of their contract prior to the late payment, effectively invalidating the agreement.
"Samsung breached the License Agreement last fall by refusing to make its Fiscal Year 2 royalty payment on time and then refusing to pay interest on its late payment and is threatening to breach the License Agreement again with respect to its ongoing royalty payment obligations for Fiscal Year 3 and thereafter," Microsoft claimed in the court document.
Some industry experts have suggested the ongoing legal battle is just the latest clash in what is already a strained relationship between the two companies.
In recent years, Samsung has increasingly moved away from Microsoft services and products in order to focus on the Android-powered smartphone market. Earlier this year, the South Korean firm announced that it plans to close its PC and laptop division to concentrate on mobile devices.
However, Microsoft's corporate vice president and deputy general counsel David Howard wrote in a blog post that the two firms intend to continue their partnership.
"We are confident that our case is strong and that we will be successful. At the same time, Microsoft values and respects our long partnership with Samsung, is committed to it, and expects it to continue."
Samsung does have a history of contesting court cases with other industry leaders. In 2011, the technology giant clashed with Apple over accusations of patent infringement, before eventually ceasing litigation in August of the following year.