Propagation of grape rootstocks with cuttings is one of the routine processes of viticulture. Cutting studies for nursery production under nursery conditions often fall below the expected productivity level due to biotic and abiotic stress. To increase nursery yield remains on the agenda of vine researchers. Encapsulated silver nanoparticles (AgNPs) were produced by the green synthesis method from grape seed extract (Vitis vinifera L. cv Öküzgözü) with high phenolic content and silver nitrate (AgNO). The size of AgNPs was determined by Transmission Electron Microscope (TEM) as 10–50 nm and was not agglomerated and browned in colour. The effect of AgNPs on rooting of standard lignified 41B (Vitis vinifera L. cv. Chasselas × Vitis berlandieri) rootstocks pure and with Indole 3 Butyric Acid (IBA) (control, 0.5 mg L−1 AgNPs, 0.5 mg L−1 AgNPs 50 ppm IBA, 1 mg L−1 AgNPs, 1 mg L−1 AgNPs 50 ppm IBA and 50 ppm IBA) were tested. The effects of the applications on the cuttings in the greenhouse 1:1 perlite peat medium, leaf chlorophyll content, vegetative growth parameters and the effects on the vascular tissues were evaluated by micro tomography (microCT). Applications of pure AgNPs and combined with IBA did not altered the leaf chlorophyll content. While 1 mg L−1 AgNPs application, which was the closest level to 50 ppm IBA, provided the root and shoot development, while the application of 1 mg L−1 AgNPs encouraged the development of shoot most. The 1 mg L−1 AgNPs + 50 ppm IBA application resulted in the highest number of nodes in shoots developing from cuttings. In microCT analysis of rooted and unrooted grapevine cuttings, tissue damage was determined that was attributed to result in drying due to embolism and loss of nursery material. AgNPs applications are thought to increase the nursery success in grapevine rootstock cuttings.