We study tree level one-point functions of non-protected scalar operators in the defect CFT, based on N=4 SYM, which is dual to the SO(5) symmetric D3-D7 probe brane system with non-vanishing instanton number. Whereas symmetries prevent operators from the SU(2) and SU(3) sub-sectors from having non-vanishing one-point functions, more general scalar conformal operators, which in particular constitute Bethe eigenstates of the integrable SO(6) spin chain, are allowed to have non-trivial one-point functions. For a series of operators with a small number of excitations we find closed expressions in terms of Bethe roots for these one-point functions, valid for any value of the instanton number. In addition, we present some numerical results for operators with more excitations.