Embryo development and seed germination are characterized by important alterations in nuclear and chromatin organization. It is however challenging to analyze these dynamic changes because the Arabidopsis embryo is embedded in the seed coat and a layer of endosperm tissue and is therefore difficult to access. Here, we describe a protocol to analyze nuclear organization in whole-mount dry seed embryos from Arabidopsis thaliana and to investigate the distribution of histone variants and modifications using immunostaining on isolated embryo nuclei. This protocol should be useful to elucidate the dry seed-specific chromatin organization and to follow dynamic changes in nuclear organization during seed germination.