Wings Over Scotland founder Stuart Campbell, who has raised more than £150,000, made the decision following discussions with the watchdog.
He said at the time of the fundraising that he would use the cash to print a pro-independence booklet for thousands of voters - an activity governed by referendum legislation.
The move raises questions about whether well-funded web activists will become a formal part of the campaign.Yes Scotland, Better Together and political parties are constrained by spending limits from May 30 until referendum day. Third-party groups such as businesses and unions must register if their campaign spending exceeds £10,000, with a £150,000 ceiling.
Newspapers are exempt, but a grey area exists over online activists who combine campaigning and journalism.
Wings Over Scotland offers trenchant political commentary and critiques of the media. The blog has also attracted financial support: it raised about £45,000 in 2013 and around £111,000 earlier this year, which exceeded a £50,000 target. Before this year's fundraising drive, Campbell gave a breakdown of how he would spend the £50,000, including £19,890 for a salary, £3000 for running costs, £4000 for contributors and £3000 for using a fundraising site.
Other spending items included polling and printing pro-independence materials.
Campbell said he could use surplus - which was more than £60,000 - on more printed materials, Q&As with undecided voters and promotional work such as billboards.
Referendum rules state that advertising, unsolicited material to voters, market research, rallies and events count as campaigning.
Campbell confirmed that Wings will register as a formal campaigner. His intention to print and distribute a pro-independence booklet is the reason behind the decision.
Campaigners are also required to declare details of their donors.
Registered third parties that support a Yes vote include Business for Scotland, Women for Independence, National Collective, Generation Yes and the Scottish Independence Convention. The No Borders campaign is registered to campaign for a No vote.
Campbell said: "We've been in conversation with the Electoral Commission since March and expect to be registering as permitted participants very shortly. Journalism is exempt from the rules, but we're also going to be producing campaigning materials and possibly undertaking some live events, and those will be subject to the spending regulations. We're looking forward to the benefits of official participant status, such as having Wings Over Scotland observers at all the referendum counts."
An Electoral Commission spokesman said: "We have had conversations with Wings Over Scotland about the rules regarding campaigning at the referendum and what they need to consider should they wish to become a permitted participant at the referendum."
A Better Together spokesman said: "This is the correct decision. Anyone spending substantial sums of money campaigning must register and then be transparent about who is funding them."