Under a longstanding tradition, the Netherlands donated some 50,000 tulips, daffodils, roses and orchids for the occasion.
Access to the famous square for the mass on the holiest day in the Christian calendar, marking Jesus's resurrection, was tightly controlled.
Tourists and clergy alike formed long queues to have their belongings checked and pass through metal detectors.
"Rome is the centre of the Catholic faith," anti-terror prosecutor Federico Cafiero de Raho said Saturday.
"For those who believe in the radical form of holy war, Rome represents so many things put together -- there's the pope, the Vatican..."
Italian authorities are concerned that some of the estimated 120 radicalised Italians who left for Syria or Iraq to fight with jihadist groups could be returning to the country posing as migrants.
Last week saw a wave of anti-terror arrests, with Interior Minister Marco Minniti warning of a high risk of an attack.
At noon (1000 GMT), the pope is to deliver his traditional "Urbi et Orbi" (To the City and the World) address from the balcony of St Peter's Basilica.
The head of the world's 1.2 billion Catholics is expected to touch on many of the world's conflicts and woes in the speech carried by news media around the globe.
On Good Friday, Francis said he was "ashamed" that younger generations would inherit a world "fractured by divisions and wars".
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