Lanthanoid complexes are amongst the most promising compounds both in single ion magnetism and as molecular spin qubits, but their organization remains an open problem. We propose to combine Lanthanide Binding Tags (LBTs) with recombinant proteins as a path for an extremely specific and spatially-resolved organisation of lanthanoid ions as spin qubits. We develop a new computational subroutine for the freely available code SIMPRE that allows an inexpensive estimate of quantum decoherence times and qubit–qubit interaction strengths. We use this subroutine to evaluate our proposal theoretically for 63 different systems. We evaluate their behavior as single ion magnets and estimate both decoherence caused by the nuclear spin bath and the interqubit interaction strength by dipolar coupling. We conclude that Dy3+ LBT complexes are expected to behave as SIMs, but Yb3+ derivatives should be better spin qubits.Lanthanoid complexes are amongst the most promising compounds both in single ion magnetism and as molecular spin qubits, but their organization remains an open problem. We propose to combine Lanthanide Binding Tags (LBTs) with recombinant proteins as a path for an extremely specific and spatially-resolved organisation of lanthanoid ions as spin qubits. We develop a new computational subroutine for the freely available code SIMPRE that allows an inexpensive estimate of quantum decoherence times and qubit–qubit interaction strengths. We use this subroutine to evaluate our proposal theoretically for 63 different systems. We evaluate their behavior as single ion magnets and estimate both decoherence caused by the nuclear spin bath and the interqubit interaction strength by dipolar coupling. We conclude that Dy3+ LBT complexes are expected to behave as SIMs, but Yb3+ derivatives should be better spin qubits.