Seventeen apartment buildings were evacuated after an explosive device was found in the city near the Ukraine border.
Two days earlier, a Russian warplane accidentally dropped a bomb on the city, damaging local houses, authorities said.
Those evacuated lived in the same area.
The city is located about 40km (25 miles) from the border with Ukraine.
Military explosive experts decided to “neutralise” the explosive at a training ground, Belgorod Governor Vyacheslav Gladkov wrote on Telegram.
“The operational headquarters decided to evacuate 17 apartment buildings within a radius of 200 metres. According to preliminary data, it is more than 3,000 people. Anyone who needs help with temporary accommodation, it will be provided,” he said.
The precautionary evacuations ended later in the day, according to Belgorod Mayor Valentin Demidov.
“The bomb was removed from the residential area. Residents are being delivered back to their homes,” Demidov wrote on Telegram.
On Thursday, a Russian Sukhoi-34 supersonic warplane accidentally fired a weapon into Belgorod, causing an explosion and injuring three people, Russian officials said.