The effect of ventilation during the multiplication stage on the development of propagules from different clones of jojoba [Simmondsia chinensis (Link) Schneider] was investigated. Variation in the response to ventilation was due to genotype, the extent of ventilation, and to the period of exposure (transfer number). With intermediate ventilation treatments, propagules elongated to a greater extent and produced more dry biomass than propagules grown without ventilation. In the highest ventilation treatment, however, growth parameters were negatively affected. More importantly, propagules grown with moderate ventilation produced more plant material suitable for further multiplication and for the elongation stage than those grown in sealed tubes—the vessels used in our original micropropagation system. In five of the seven clones studied, growth and multiplication rate were decreased by the highest ventilation treatment. Propagules from the second and third multiplication transfers into ventilated vessels became more sensitive to high ventilation. Ambient water loss was slower in propagules produced under ventilation, probably due to smaller stomatal apertures. As a result of improved growth and decreased hyperhydricity by ventilation, the micropropagation protocol should be modified to include Magenta boxes equipped with vented lids as the preferred growing vessels.