We analyse the Kormendy relations (KRs) of the two Frontier Fields clusters, Abell S1063, at z=0.348, and MACS J1149.5+2223, at z=0.542, exploiting very deep Hubble Space Telescope photometry and Very Large Telescope (VLT)/Multi Unit Spectroscopic Explorer (MUSE) integral field spectroscopy. With this novel data set, we are able to investigate how the KR parameters depend on the cluster galaxy sample selection and how this affects studies of galaxy evolution based on the KR. We define and compare four different galaxy samples according to (a) Sersic indices: early-type ('ETG'), (b) visual inspection: 'ellipticals', (c) colours: 'red', (d) spectral properties: 'passive'. The classification is performed for a complete sample of galaxies with m_F814W_<=22.5-ABmag (M_*_>=10^10.0^M_{sun}_). To derive robust galaxy structural parameters, we use two methods: (1) an iterative estimate of structural parameters using images of increasing size, in order to deal with closely separated galaxies and (2) different background estimations, to deal with the intracluster light contamination. The comparison between the KRs obtained from the different samples suggests that the sample selection could affect the estimate of the best-fitting KR parameters. The KR built with ETGs is fully consistent with the one obtained for ellipticals and passive. On the other hand, the KR slope built on the red sample is only marginally consistent with those obtained with the other samples. We also release the photometric catalogue with structural parameters for the galaxies included in the present analysis.