This study aimed to identify whether the positive effects found in the germination time of the magnetically treated tomato seeds are conserved until the vegetative stage, and how the value of morphological parameters change. Tomato plants were analyzed in a greenhouse during the vegetative stage. A longitudinal study was carried out using a repeated-measures design over time, complemented by a correlational transectional study through principal component analysis. Briefly, 225 experimental units were divided into three treatments of 75 plants each. Leaf area, stem diameter, height, number of leaves, and chlorophyll content were recorded twice weekly. A longitudinal study showed that magnetic treatment continuously modified the structure and biomass accumulation of plants throughout the vegetative stage. Plant height, stem diameter, and leaf number were directly and independently correlated with time, whereas chlorophyll content and leaf area were time-dependent. Biophysical and biochemical modifications induced by magnetic seed treatment during germination modulated all the measured variables during the vegetative stage. Thus, our data suggest that plants generated from magnetically treated seeds have higher nutrient requirements.