In this paper, we start by showing that the intertwining relationship between two minimal Markov semigroups acting on Hilbert spaces implies that any recurrent extensions, in the sense of Itô, of these semigroups satisfy the same intertwining identity. Under mild additional assumptions on the intertwining operator, we prove that the converse also holds. This connection, which relies on the representation of excursion quantities as developed by Fitzsimmons and Getoor, enables us to give an interesting probabilistic interpretation of intertwining relationships between Markov semigroups via excursion theory: two such recurrent extensions that intertwine share, under an appropriate normalization, the same local time at the boundary point. Moreover, in the case when one of the (non-self-adjoint) semigroup intertwines with the one of a quasi-diffusion, we obtain an extension of Krein's theory of strings byshowing that its densely defined spectral measure is absolutely continuous with respect to the measure appearing in the Stieltjes representation of the Laplace exponent of the inverse local time. Finally, we illustrate our results with the class of positive self-similar Markov semigroups and also the reflected generalized Laguerre semigroups. For the latter, we obtain their spectral decomposition and provide, under some conditions, a perturbed spectral gap estimate for its convergence to equilibrium.