The midday flight took off from San Juan at 10:29 a.m., but ended up having to alter its course shortly into the flight and landed in Fort Lauderdale just before 1 p.m.
"JetBlue flight 1052 from San Juan to Tampa diverted to Fort Lauderdale in an abundance of caution following a report of damage to one of the outer layers of the cockpit windscreen," JetBlue said in a statement. "The flight landed safely at approximately 1:00 p.m. local time. Customers have been accommodated on another aircraft."
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The cracks did not cause the plane to lose cabin pressure.
Passengers changed planes and eventually arrived in Tampa at 3:31 p.m., according to Tampa ABC affiliate WFTS.