Flights were scheduled to resume at Ngurah Rai International Airport after 3 p.m. local time (3 a.m. ET), after the Volcano Observatory Notice for Aviation was downgraded from a Red alert to Orange.
While the decision will be a relief to tens of thousands of stranded tourists, uncertainty still remains for evacuated locals amid fears of further eruptions and destroyed crops.
Indonesia's National Board for Disaster Management (BNPB) have estimated as many as 100,000 people could be living in the evacuation zone, with more than half still remaining in their homes.
At a refugee shelter in Rendang, 25-year-old farmer Komang Suterni told CNN her flower crop had been destroyed by the ashes.
"I have nothing left ... I hope my son gets donations from the government," she said, cradling her 7-month son Kadek.
On Wednesday morning, the volcano continued to belch black smoke into the surrounding area, amid fears another larger eruption could still occur.
The BNPB maintained a Level 4 warning Wednesday, the highest alert level possible. It was initially raised on Monday morning.
Authorities are continuing to call for evacuations from the area around the volcano, as well as banning all recreational activities within 10 kilometers of the crater.
Emergency workers were going to villages on Tuesday calling for people to leave the danger zone, but the BNPB said they were encountering resistance from people concerned about their livestock and belongings.
Refugee Mangku Wayan Sugita said the area around his entire village was affected by the volcano.
"All covered by volcanic ash that come down to the ground, the grass everything," he said, adding he'd already gone back despite the warnings.
The main tourist centers are some distance from Mount Agung. Bali's artistic hub, the small town of Ubud, is about 50 kilometers (31 miles) southwest of the volcano, and Denpasar (where the airport is located) and the popular Kuta Beach are more than 63 kilometers (40 miles) away.
Spokesman for the BNPB Sutopo Purwo Nugroho said Tuesday growing seismic activity around Mount Agung indicated another eruption could occur soon, but no further announcements have been made since.
CNN's Chieu Luu and Hendra Brawijaya contributed to this report.