In the present paper we develop the algebraic Bethe ansatz approach to the case of non-skew-symmetric gl(2)⊗gl(2)-valued Cartan-non-invariant classical r-matrices with spectral parameters. We consider the two families of these r-matrices, namely, the two non-standard rational r-matrices twisted with the help of second order automorphisms and realize the algebraic Bethe ansatz method for them. We study physically important examples of the Gaudin-type and BCS-type systems associated with these r-matrices and obtain explicitly the Bethe vectors and the spectrum for the corresponding quantum hamiltonians in terms of solutions of Bethe equations.