Causes of secondary sexual dimorphism (SSD) in dioecious plants are very poorly understood, especially in woody plants. SSD is shown mainly in mature plants, but little is known about whether secondary sexual dimorphism can occur in juveniles. It is also assumed that stress conditions intensify differences between the sexes due to the uneven reproductive effort. Therefore, the following research hypotheses were tested: (1) secondary sexual dimorphism will be visible in juveniles; (2) unfavourable soil conditions are the cause of more pronounced differences between the sexes. Rooted shoots of the common yew (Taxus baccata L.) and common juniper (Juniperus communis L.), previously harvested from parental individuals of known sex were used in the study. During two growing seasons vegetation periods and four times a year, comprehensive morphological features of whole plants were measured. Some SSD traits were visible in the analysed juveniles. Contrary to expectations, differences were more pronounced in the fertilized treatment. Both species reacted to fertilization in different ways. Female yew had a clearly higher total plant mass, root mass, and mean root area when fertilized, whereas male juniper had a higher root mass when fertilized. Differences between the sexes independent of the fertilization treatment were seen, which can be interpreted as sexual adaptations to a continued reproduction. Female yews and male junipers made better use of fertile habitats. Our study showed that SSD may be innate, and sexual compensatory mechanisms could generate uneven growth and development of both sexes. Because the SSD pattern was rather different in both species, it was confirmed that SSD is connected with the specific life histories of specific species rather than a universal strategy of dioecious species.