Background: Zr region is characterized by very rapid changes in the ground state structure of the nuclei. In particular, the onset of deformation when passing from $^{98}$Zr to $^{100}$Zr is one of the fastest ever observed in the nuclear chart. It has been probed both experimental and theoretically that certain low-lying excited states of Zr isotopes own different shapes than the ground state. Purpose: We intend to disentangle the interplay between the sudden changes in the ground state shape, i.e., the existence of a quantum phase transition, and the presence in the spectra of coexisting states with very different deformation, i.e., the presence of shape coexistence. Method: We rely on a previous calculation using the Interacting Boson Model with Configuration Mixing (IBM-CM) which reproduces in detail the spectroscopic properties of $^{96-110}$Zr. This IBM-CM calculation allows to compute mean-field energy surfaces, wave functions and any other observable related with the presence of shape coexistence or with a quantum phase transition. Results: We obtain energy surfaces and the equilibrium value of the deformation parameter $beta$, the U(5) decomposition of the wave functions and the density of states. Conclusions: We confirm that Zr is a clear example of quantum phase transition that originates from the crossing of two configurations with a very different degree of deformation. Moreover, we observe how the intruder configuration exhibits its own evolution which resembles a quantum phase transition too.