Spatial transcriptomics technologies have made enormous progress in terms of outputs and resolutions, helping scientists comprehend the complexity and heterogeneity of multicellular organisms. Due to the cost of commercially available kits and technical difficulties for in-depth coverage which requires multiple consecutive tissue sections, the application and development of these technologies to obtain high-resolution 3D whole-mount plant data is lagging behind. A cost-effective and high-resolution technique to analyse in-depth and in detail where and when exactly transcripts are expressed in native spatial cellular context is needed. PHYTOMap is a targeted multiplexed FISH technology developed for Arabidopsis roots that allows single-cell and spatial gene expression analysis in 3D whole-mount tissue in a transgene-free manner. We optimised this spatial transcriptomics technology for Arabidopsis seed by manual dissection of embryos, optimising sample clearing and retention, probe concentration for optimal imaging, and subsequent confocal microscopy to generate higher resolution images. We applied PHYTOMap for the first time in seeds, allowing us to validate our previously published single-cell transcriptomics data of germinating seeds. It confirms cell state-specific gene expression at subcellular resolution within the native 3D tissue context of germinating embryos. This allows us to precisely localise and quantify the level of transcripts during germination to build accurate co-expression and gene regulatory networks. This will help us to better understand the establishment of unique functions of different cell types and their spatial interactions during the highly dynamic cell states transition happening in germinating seeds.