More than 155,000 people voted to re-elect the charismatic 38-year-old as chief and a large majority of his list of candidates for the leadership council.
They also backed his strategy for the future of Podemos, in what supporters hope will end months of in-fighting in one of Europe's leading far-left parties.
More than 89 percent of voters backed Iglesias as secretary general, while 56 percent endorsed his vision for Podemos, in results that met with wild applause from thousands of Podemos followers gathered in a conference centre in Madrid, who shouted "yes we can" and "unity".
Born in 2014 out of the Indignados protest movement that swept Spain during a severe economic crisis, Podemos, an ally of Greece's Syriza, experienced a meteoric rise to national-level politics, winning millions of votes in two elections to become the country's third party.
Buoyed by promises of radical change and a more egalitarian society, Podemos won 71 seats in parliament as part of a wider leftwing coalition.
But it found itself at a crossroads that divided its pony-tailed chief and his deputy and once close friend Inigo Errejon, creating a rift in the entire party over how to achieve its goal of replacing the Socialists as the main opposition party, and eventually take power.
Should Podemos, which harnessed the anger of millions stung by Spain's economic woes, take to the streets again as an anti-establishment group, as wanted by Iglesias?
Or should it shed an "enfant terrible" image that may be scaring away voters now that it has become a credible political force, and work from within parliament as Errejon proposed?
In the end, activists made the final decision.
"It's good because we now have clarity," Podemos co-founder and lawmaker Carolina Bescansa, who has stayed out of the in-fighting, told AFP.
The split between Iglesias and his number two erupted into the open last year, playing out on social media and in the press.
Supporters, who looked on with dismay, are hoping the rift will be put to rest now the results have been announced.
Iglesias was almost assured of being re-elected given he was only up against a low-profile lawmaker, but his list of candidates for the leadership council met with stiff competition.
Errejon had presented his own list, as did other popular Podemos members such as Teresa Rodriguez, a regional Podemos lawmaker in southern Andalusia,and MEP Miguel Urban.
As such, Iglesias had said that if his list was rejected, he would step aside, precipitating another crisis for a party that would be left without the public face of the Podemos success story.
The new leadership council is composed of a majority of those on Iglesias's list, even if some of Errejon's team are also included, including the number two himself.
On Sunday, Iglesias hugged each of the new members of the council on a stage flanked by purple flags, the colour of Podemos.
He took an extra minute to embrace Errejon, who gave a weak smile.
Iglesias and Errejon have pledged that come what may, it will be business as usual for Podemos from Monday, putting the divisions firmly behind them.