At least 20,000 visas a year will likely be issued, primarily to Cubans trying to reach family members in the US.
The reopening comes amid a record exodus from the island, as Cuba suffers one of its worst economic crises.
Consular services were reduced to a minimum under the Trump Administration.
The services were closed in 2017 following reports of unexplained health incidents among embassy employees, which eventually became known as the "Havana Syndrome".
The syndrome was initially noted among US intelligence officers and diplomats in the Havana embassy - before being reported in other parts of the world - who first began complaining of an array of unusual symptoms about seven years ago.
Many theories behind the illnesses have been now debunked but the full causes remain unclear.
The news of resumption of visa services, announced last week by the embassy, will come as relief for thousands of Cubans who are desperate to see their families in Florida and elsewhere in the US.
The step comes as Cuban migration to the United States is reaching levels not seen in decades. Under a bilateral agreement, the US will issue at least 20,000 visas a year to Cubans.
However, that is a tiny proportion of those who are leaving or trying to leave. Border authorities in the US recorded around 225,000 Cubans entering the country illegally last year.
After 2016, the Trump Administration implemented a whole raft of new economic sanctions on the communist-run island, following the easing of the same rules by President Barack Obama.
Combined with the economic downturn from the coronavirus pandemic and economic mismanagement by the state, the economy in Cuba has been in dire straits in recent years.
The US government recently announced plans to ease tough sanctions imposed on Cuba by former President Trump.
Under new measures approved by the Biden administration, restrictions on family remittances and travel to the island will be eased.