Despite having grown up in Japan, she handles English fluently.
Literal
She [topic-は] Japan [in-で] grew-up [despite-にもかかわらず], English [object-を] [freely-自由に] uses-and-masters.
Two notable features. ~にもかかわらず ('despite') marks an unexpected contrast — Japan-raised, yet English-fluent. 使いこなす is a compound verb: 使う ('use') + こなす ('handle, manage'), giving 'master the use of, handle skillfully.' The ~こなす auxiliary is productive: 着こなす ('wear stylishly'), 乗りこなす ('drive masterfully').