It comes after a sweltering summer where temperatures regularly topped 40C and felt even higher, with drought and wildfires across Italy.
Two weather fronts, or air masses, are on their way to the peninsula, bringing lower temperatures and heavy rains between Friday and Monday.
The south of the country is expected to feel the brunt of the bad weather on Friday, with the Civil Protection Agency warning of "widespread and intense thunderstorms" in Sicily, Calabria, and Campania, before spreading to affect Puglia and Basilicata from late morning as well.
Temperatures are forecast to fall well below the seasonal average, with highs between 24-28C.
Basilicata was placed on orange alert (moderate) for hydrogeological risk, while several other parts of the northeast and south were on yellow alert (ordinary level of criticality).
Alerts in place on Friday. Image: Civil Protection Agency
"The phenomena will be accompanied by torrential rains, lightning, hail, and strong gusts of wind," the agency said.
On Saturday, heavy rains are predicted for all the north and south of the country, but the central regions and islands should be spared.
In the below image shared by the Civil Protection Agency, dark blue shows very high levels of rainfall, while the turquoise shades show moderate and light levels. Red lightning bolts mark areas where storms are expected.
Alerts in place on Saturday. Image: Civil Protection Agency
On Sunday, storms are expected to continue in the northeast, centre, and the islands. Particularly heavy rainfall (up to 100 litres per square metre) is forecast for the central Alps, Venice, and areas of Tuscany, Lazio, and Campania.
Temperatures in the south will start to creep back up, possibly topping 30C, but in the north there will be a further drop, even falling below 20C in some places, according to the meteorologists at 3bMeteo.