The epidermis is the outer layer of the skin, which protects us against the hostile environment and keeps bodily fluid inside. Along with interfollicular epidermis, which makes up the protecting barrier, various adnexal structures such as pilosebaceous units provide auxiliary functions. Previous work from our group has shown that the epidermis is compartmentalized into distinct functional units, which are maintained autonomously by resident epidermal stem cells. This normal behavior is abruptly altered upon injury, as natural compartment borders are rapidly eroded in order to facilitate tissue repair. We now show that during tissue morphogenesis, these self-maintained epidermal tissue compartments are established by lineage committed stem cells. Clonal lineage tracing in multicolour reporter mice followed by biophysical modeling of the dynamical changes in clone size, 3D composition and distribution in upper pilosebaceous units reveal that compartmentalisation into distinct functional units occur prior to the formation of actual physical tissue compartments with mature functions. During homeostasis the individual compartments are subsequently maintained at a compartment specific pace and balanced growth factor signaling appears to control compartment size. Our results feed directly into a broader understanding of the underlying machinery that dictates tissue integrity and more specifically, how this is set up during morphogenesis and tissue homeostasis. Such knowledge is essential for the development of therapeutic tools that can reset tissue homeostasis in devastating diseases such as cancer.