More than 340 political parties across the UK submitted their annual statements of accounts to the commission on time. However, the Scottish Greens were among seven who failed to do so, the commission confirmed.
This breach can lead to fines and further sanctions if the commission believe there is further wrongdoing.
The Scottish Greens told The Scotsman their accounts have now been submitted with a clean audit report.
The party is set to enter government with the SNP should the co-operation deal agreed by the leaders of the two parties be ratified by the Scottish Greens’ membership.
The SNP is also undertaking a consultative ballot of its members to understand levels of support for the deal.
Co-leaders of the Greens, Patrick Harvie and Lorna Slater, will receive ministerial roles in the government should the deal be agreed by their party members.
The MSPs will be given remits covering decarbonising transport, homes and buildings as well as a new deal for tenants, with another looking at green skills and industries such as the energy sector.
Louise Edwards, director of regulation at the Electoral Commission, said: “All registered political parties must keep financial records and submit annual statements of accounts to us. Publishing this data helps voters see political parties’ income and what they’re spending.
"This is an important part of delivering transparency in political finance in the UK, and in enhancing public confidence and trust in our democratic processes.”