Seed germination and early root growth are decisive for crop establishment, yet responses to ionic environments can be strongly genotype-dependent. This study evaluated the effect of supplementing an agar-based in vitro system with a commercial NPK fertilizer on the germination dynamics and early morphometry of Raphanus sativus L. Three commercial varieties were tested (Agrosad, AS; Agrícola Santo Domingo, ASD; Garden Elite, GE) under two media: 1.5% agar without fertilizer (A) and 1.5% agar + NPK fertilizer at 3 g/L (AF), using a completely randomized 3×2 factorial design. Germination was recorded at 24, 48, and 72 h to compute final germination (%G), mean germination time (MGT), germination speed index (IVG), and coefficient of velocity of germination (CVG); root length was measured at 72 h. MANOVA (Pillai’s trace) indicated significant effects of Variety, Fertilization, and their interaction, confirming that fertilizer responses depended on genotype. While AS and GE maintained high %G (>88%) under AF, fertilization generally delayed germination (higher MGT) and reduced vigor (lower IVG). ASD showed the strongest inhibition, with %G dropping from 88.89% (A) to 25.93% (AF) and the lowest IVG (1.23). Root elongation was significantly reduced by fertilization in ASD and GE, whereas AS exhibited consistently shorter roots with no significant response. PCA summarized 86.36% of the total variance in the first two components, separating treatments along a vigour/architecture axis (IVG and root length positive; MGT negative) and a germination capacity axis (%G), and hierarchical clustering identified five response groups. Overall, a low-cost agar + fertilizer system effectively discriminated genotype-specific sensitivity to an ionic environment during early establishment, highlighting the need to consider variety-dependent thresholds when using commercial fertilizers for in vitro screening.