In vitro grafting is one of the promising techniques for fruit crop breeding. This study was performed to produce in vitro vigorous passion fruit rootstocks and developed a simple in vitro grafting protocol with the support of nylon microtubes—a low cost, wide availability, non-toxic and reusable material. The results showed that stem-lTCL explants (longitudinal thin cell layers) cultured on MS medium containing 0.5 mg/L BA and 0.5 mg/L NAA gave the highest shoot regeneration, and these shoots were initial materials for micropropagation of passion fruit rootstock. MSM medium containing 5 mg/L AgNPs increased shoot multiplication twofold higher than that of control and significantly reduced leaf yellowing and leaf drop during this stage. Rooting rate and quality of the plantlets were optimal on MSM medium contained with 2.5 mg/L IBA as well as their survival rate was enhanced in nursery. Nylon microtubes improved the efficiency of passion fruit in vitro grafts to 73.33% with yellow passion fruit as rootstock and purple passion fruit nodal segments as scion. In addition, the use of nylon microtubes significantly improved the in vitro growth of in vitro grafted plants resulting in increased survival rate and plantlet growth in the nursery stage. The present results provide an efficient protocol for micropropagation of yellow passion fruit for rootstock and production of purple passion fruit via nylon microtubule-mediated in vitro grafting. Key message An efficient protocol was established for multiplication of in vitro vigorous passion fruit rootstock via the application of thin cell layer culture techniques, nanotechnology and modification of the culture medium. Nylon microtubes enhanced the success rate of in vitro grafting and ex vitro grafted plant growth.