Using an internet portal called "Rousseau" after the 18th-Century French philosopher, M5S uses online votes of members to decide its policies, draft legislation and candidates.
Created by the late Gianrobert Caleggio, a computer expert who co-founded the movement with comic Beppe Grillo in 2009, the platform is presented by the party as a reflection of its unique commitment to grassroots democracy and a new politics untainted by Italy's long tradition of behind-the-scenes, self-serving deals among an exclusive political class.
But it has become increasingly criticised, notably by former members, for its lack of transparency and the party leadership's tight control over how it works.
And as M5S seeks to fight an ever larger number of elections at every level, its use in the selection of candidates, typically on the basis of one short video post, has also come under scrutiny.
Virginia Raggi, 37, was elected mayor of Rome in June 2016 after being plucked from relative obscurity to join a long list of 200 potential M5S candidates.
The photogenic lawyer shone on the small screen and won the selection battle.
But in office her lack of experience has been exposed as the new administration has lurched from one crisis to another.
With little sign of the movement demonstrating it can address the capital's myriad problems this has led to tensions between Raggi and Grillo, who has been branded a control freak tyrant by rivals in Italy's mainstream parties.
In Genoa, Grillo's home town, Marika Cassimatis topped the movement's poll of activists only to be struck off the list when the leader deemed her positions on certain issues, and some of her backers, to be "contrary to the principles of the movement."
He then compounded the damage caused by that incident by adding on his blog: "I'd ask anyone who does not understand this decision just to trust to me."
That proved to be the final straw for some activists who quit the movement in its first significant defections.
"What the M5S shows us is that electronic democracy does not work, notably because it can be subject to all sorts of manipulation, either technological or ideological," said Leonardo Morlina, a political science professor at Rome's social studies university.
"The Genoa example was symptomatic. We don't really know why the choice of candidates was not approved. We just have Beppe Grillo's explanation to go on, which poses a problem for internal party democracy.
Anti-euro and anti-immigration but also with a green tinge to some policies, M5S emerged as a major political force in the 2013 general election when it snapped up 25.5 percent of the vote, becoming the second biggest political force behind the PD.
It has built on that level of support since and last year won control of Rome and Turin as well as a string of smaller municipalities.
Polls suggest it could win around 30 percent of the popular vote when the next election is held, most likely early next year.
But the University of Bologna's Gianfranco Pasquino thinks the appeal of its supposed ultra-democratic structure is limited.
"The number of people involved in these online votes makes up a very small proportion of the electorate. From the democracy perspective, they are of very little interest."
Despite its millions of supporters, only 140,000 people are registered on "Rousseau" and less than a quarter of them participate in votes, on average.
"It is not a party it is an algorithm," former prime minister Matteo Renzi recently joked.
M5S has also been hit recently by allegations of involvement in propagating "fake news" via its extensive network of websites, including items favourable to Russia and Donald Trump or lending credence to various conspiracy theories.
"But so far this has not had any impact on Five Star's core support," emphasises Pasquino. "Their rejection of the traditional parties is so strong it seems Five Star's level of support is currently strongly underpinned."