The center of the storm, which was downgraded from a Category 1 hurricane, made landfall in Taylor County along the Gulf Coast of northern Florida, according to the National Hurricane Center.
Elsa was logged as the first hurricane of this year's Atlantic season before being downgraded to a tropical storm again
According to the NHC, Elsa was lashing in with a maximum sustained wind speed of 50 miles per hour (85 kilometers per hour) at 2:00 pm local time (1800 GMT). The weakening of the storm is expected to continue through Thursday as Elsa moves over land into the country on a northern trajectory.
Tampa airport in Florida suspended commercial flights from Tuesday into Wednesday in preparation of the landfall, but the storm ended up hitting well to the north of the third-largest city in the state.
The NHC warned that the western and northern portions of the Florida Peninsula are expected to get between three and six inches of rain. If the warning turns out to be true, the area could see a considerable amount of flooding.
NHC also said that tornadoes were possible on Wednesday in northern Florida, southeastern Georgia and eastern South Carolina.
Florida Governor Ron DeSantis urged residents to take precautions.
"This is not a time to joyride. You do have hazardous conditions out there," AFP quoted DeSantis as saying.
Lieutenant Governor Jeanette Nunez called on Floridians to be prepared for the possibility of power blackouts and to stockpile adequate supplies of food and water.
Over the weekend, Elsa battered Jamaica and Cuba, claiming at least three lives as it cut a path of destruction through the Caribbean.
Elsa claimed two lives in the Dominican Republic and a third in the island state of Santa Lucia, the Caribbean Disaster Emergency Management Agency said.
Elsa had threatened to complicate an already challenging search mission for survivors of the June 24 deadly condo tower collapse in Surfside, a town north of Miami Beach on Florida's east coast.
But the storm made landfall on the opposite coast allowing search teams to continue their work largely interrupted although the search operations were ended on Wednesday. The recovery work will continue.
The confirmed death toll from the condo disaster rose to 46 on Wednesday with the discovery of 10 more bodies. A total of 94 people are still listed as missing.