We address the computational spectral theory of Jacobi operators that are compact perturbations of the free Jacobi operator via the asymptotic properties of a connection coefficient matrix. In particular, for finite-rank perturbation we show that the computation of the spectrum can be reduced to a polynomial root finding problem, from a polynomial that is derived explicitly from the entries of a connection coefficient matrix. A formula for the spectral measure of the operator is also derived explicitly from these entries. The analysis is extended to trace-class perturbations. We address issues of computability in the framework of the Solvability Complexity Index, proving that the spectrum of compact perturbations of the free Jacobi operator is computable in finite time with guaranteed error control in the Hausdorff metric on sets.