The commercial production of walnut plants still relies on field or greenhouse grafting using seedling plants as rootstocks. This is a time-consuming process, requiring at least two years to produce a grafted plant, and often results in orchard heterogeneity, thereby complicating mechanization procedures. In recent years, in vitro micropropagation has enabled the clonal propagation of walnut cultivars and rootstocks; however, grafting practices remain largely dependent on traditional nursery methods. In vitro micrografting, based on the use of in vitro produced rootstocks and scions, may significantly reduce the time required to produce a grafted walnut plant. In this study, in vitro regenerated shoots of ‘Paradox’ (Juglans hindsii × Juglans regia) cl. ‘Vlach’ were used as rootstocks for micrografting, while J. regia cvs. ‘Chandler’ and ‘Howard’ were used as scions. Two cleft grafting types, top and side, were tested across three developmental stages of the rootstock (pre-rooting, post-rooting, and post-acclimatization). The results showed that for both cleft grafting methods and for the two cultivars, no statistically significant differences were found. In contrast, statistically significant differences emerged among the different phases in which micrografting was performed. The highest grafting success was achieved with cv. ‘Howard’ using the side cleft method during the pre-rooting phase of rootstock development. Although further optimization is required, the results highlight the potential of in vitro micrografting as an alternative to conventional grafting methods.