We prove a higher-dimensional Chevalley restriction theorem for orthogonal groups, which was conjectured by Chen and Ngô for reductive groups. In characteristic p>2, we also prove a weaker statement. In characteristic 0, the theorem implies that the categorical quotient of a commuting scheme by the diagonal adjoint action of the group is integral and normal. As applications, we deduce some trace identities and a certain multiplicative property of the Pfaffian over an arbitrary commutative algebra.