Flags on public buildings were raised at 9am on Wednesday as the period of mourning for Sheikh Khalifa ended.
The Ministry of Presidential Affairs said the 40-day period concluded on Tuesday night.
Sheikh Khalifa died on May 13 at the age of 73.
Work across the country was suspended for three days immediately after his death.
Flags had remained at half-staff since. This period was intended as a mark of respect and life across the UAE took on a more sombre tone.
Sheikh Khalifa was the country's second president after UAE Founding Father, the late Sheikh Zayed bin Sultan Al Nahyan.
Sheikh Mohamed was elected President by the Federal Supreme Council last month.