The move came hours after Baku said it arrested six men, who it said were linked to Iranian secret services and were allegedly plotting a coup in the Caspian nation.
Azerbaijan has announced the expulsion of four employees of Iran's embassy after months of diplomatic tensions between Baku and Tehran.
The foreign ministry in Baku said on Thursday it "summoned" Iran's ambassador and told him that "four employees of the Iranian embassy were declared persona non grata" with 48 hours to leave the country.
It said they were carrying out activities "incompatible with diplomatic status" but did not provide further details.
"During the meeting, strong dissatisfaction was expressed to the Iranian Ambassador due to the recent provocative actions demonstrated by his country," the ministry added.
Earlier in the day, Baku said it arrested six Azerbaijani nationals, who were "recruited by Iranian secret services to destabilise the situation in the country".
It announced the arrests in a joint statement by the interior ministry, state security service and prosecutor-general's office.
READ MORE: What a dust-up with Azerbaijan tells us about Iran's foreign policy
Embassy attack
It accused them of being "engaged in a pro-Iranian propaganda of religious radicalism, fulfilling orders from abroad to undermine Azerbaijan's tradition of tolerance".
In January, Azerbaijan suspended the operation of its embassy in Iran, days after a gunman stormed the mission, killing one guard and wounding two others.
Baku has claimed that Tehran's secret services were behind the attack.
Last year, the oil-rich country arrested five of its nationals for spying for Iran and 17 more men who Baku claimed belonged to an "illegal armed group set up by Iran".
Azerbaijan has criticised Iran over backing Armenia in Baku's decades-long conflict with Yerevan over the breakaway region of Karabakh.
The neighbours share a border that runs near the Caspian Sea.
The tensions come as Iran is normalising ties with Saudi Arabia after a surprise China-brokered deal last month to restore diplomatic relations that were severed seven years ago.
READ MORE: Armed attack targets Azerbaijan's embassy in Iran