Ukraine's anti-corruption bureau Nabu and specialised anti-corruption prosecutor's office (Sap) did not explain why they searched his flat.
In the past few weeks investigators have linked several high-profile figures to an alleged $100m (£75m) embezzlement scandal in the energy sector. They said they had uncovered an extensive scheme to take kickbacks and influence state-owned companies including state nuclear energy firm Enerhoatom.
Russian officials involved in Trump's draft peace plan have talked up the corruption claims, which have alarmed European Union allies. Ukraine is a candidate to join the EU and a report earlier this month highlighted doubts over "commitment to its anti-corruption agenda".
Earlier this year Zelensky sought to curb the powers of the two anti-corruption agencies, but he was forced to backtrack almost immediately after widespread protests and objections from Kyiv's Western allies.
Zelensky has already fired Energy Minister Svitlana Grynchuk and Justice Minister Herman Halushchenko and several suspects have been detained in the burgeoning corruption scandal that has outraged public opinion because of allegations that money was diverted from key infrastructure projects vital for safeguarding Ukrainian power supplies.
As winter starts in Ukraine, Russian attacks have already badly damaged its energy infrastructure and Ukrainians across the country have had to cope with only a few hours of electricity a day.
One of the president's former business associates, Timur Mindich, has left the country in the wake of the corruption allegations.
Mindich was co-owner of the TV studio Kvartal 95 where Zelensky's acting career took off before he was elected president.
In recent weeks Andriy Yermak's popularity has nose-dived and MPs from all parties, including his own, have been calling for his sacking, initially for what they saw as his inflated power for an unelected official, but more recently, the burgeoning corruption scandal.
Recent polling suggested 70% of the public wanted him to resign.
Zelensky and his now-former chief of staff became friends about 14 years ago, while the future president was a senior media executive and Yermak worked for him as a lawyer. Yermak was made chief of staff a year after Zelensky was elected president in 2019.
On the first night of Russia's invasion, they appeared together with colleagues delivering a defiant video message outside the presidential office on Kyiv's Bankova Street, vowing to stay and fight.
"We are all here," Zelensky told Ukrainians. "Our soldiers are here, the citizens are here and we are all here. We are defending our independence, and that's how it will continue."