She was shy by nature.

Literal

She [topic-は] by-nature shy was.

内気 (うちき) means 'shy,' 'introverted,' or 'timid' — literally 内 (inner) + 気 (spirit/energy), suggesting someone whose energy is turned inward. 生まれつき marks this as an innate trait. The past tense だった suggests this is describing her as she was — possibly she's changed since.