The Central American nation is one of the few remaining countries to recognise the sovereignty of Taiwan, a list that has shrunk in recent years as Beijing moves to isolate Taipei on the international stage.
China considers democratic Taiwan part of its territory to be retaken one day, and does not allow other countries to recognise both Beijing and Taipei.
Images released by Taiwan's foreign ministry on Monday showed Giammattei being escorted by Taiwan's Foreign Minister Joseph Wu upon arriving at Taoyuan International Airport.
Before leaving for Taipei, Giammattei said he was making the trip to send a "clear message that countries have a right to self-governance".
During his visit Monday through Thursday, Giammattei is scheduled to address the congress of Taiwan and visit a technology company in Taichung, south of Taipei. He is also due to attend an event promoting Guatemalan coffee, according to the Taiwanese president's office.
On Wednesday, Beijing warned Giammattei's government "not to help evildoers and go against the general global trend and aspirations of the Guatemalan people for their own benefit."
Taiwan's foreign ministry condemned Beijing for using "extremely disrespectful remarks to insult our diplomatic ally and its head of state".
Giammattei's visit comes after a trip earlier this month by Taiwan's President Tsai Ing-wen to Guatemala and Belize -- the only other Central American country to retain diplomatic ties with Taiwan since Honduras shifted its allegiance to China last month.
On her way back to Taipei, Tsai stopped in the United States to meet House Speaker Kevin McCarthy.
In response, China staged three days of military exercises simulating targeted strikes and a blockade of the island.
Latin America has been a key diplomatic battleground for China and Taiwan since the two split in 1949 after a civil war.
Beijing has spent decades convincing Taipei's diplomatic allies to switch sides, gaining nine since Tsai took office in 2016.
Taiwan's 65-year-old ties with Paraguay are also at risk, with opposition candidate Efrain Alegre reportedly saying he would switch recognition to Beijing if elected in presidential elections on April 30.
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