This, the regulator said, was due to the late delivery of the party’s annual statement of accounts.
It is a legal requirement for any political party to submit its annual accounts on time or face a fine.
Louise Edwards, director of regulation at the Electoral Commission said: “It is important for transparency that voters have timely and accurate information about political parties’ finances. The requirements are clear, so it is always disappointing when they are not met.
“Where we find that offences have been committed, we take into consideration a range of factors when deciding the level of sanction, as set out in our enforcement policy.”
A spokesperson for the Scottish Greens said: “We regret that due to documentation from a third party being received late, our statement of accounts for 2020 was not submitted on time.
"Our accounts received a clean audit and we are confident the problem will not reoccur.”