The effect of thermal treatments on the magnetic behavior in negative (and nearly-zero) magnetostriction glass-coated amorphous microwires has been investigated. It has been shown that the magnetic properties of CoMnBSi microwires undergo significant changes during annealing both at low and high temperatures. The effect of the amorphous–nanocrystaline structure transformation has been discussed. The processes that lead to changes in the magnetic characteristics are associated with the homogenization of residual stress at a low annealing temperature and with the short-range order atomic structure relaxation at a high annealing temperature.