There is a growing demand for high quality and sustainable food in the world and this need falls within the context of the European Green Deal’s strategy “From Farm to Fork”. In order to achieve these outcomes, the use of modern and innovative technologies of plant production and protection is required. The use of nanoparticles (NPs) in agriculture and horticulture is an example of such technology. However, research on the effect of length of exposure to metal nanoparticles on seeds germination and seedlings development are limited in the literature. In our study, the effect of silver (AgNPs) and gold nanoparticles (AuNPs) on the seedling growth and biochemical response of rapeseed after 7, 14 and 21 days was analyzed. In the experiments, 0, 50 and 100 ppm concentrations of NPs were used in vitro. The level of photosynthetic pigments, anthocyanins as well as other stress parameters, such as free phenolic compounds, free sugars or H2O2, decreased due to the application of both AgNPs and AuNPs at the initial culture period; however, the differences were observed in the successive weeks of exposure. The parameters were increasing, irrespective of the kind of nanoparticles; however, as for the content of free sugars and free radicals, higher values were recorded due to the effect of AuNPs. Our results showed that length of plants exposure to NPs is very important factor modifying growth and final response of seedlings. Better understanding of its influence could speed up use of NPs in agriculture and horticulture for production of high-quality plant material (e.g., to seed priming, stimulation of seedlings’ growth and their protection), not contaminated with pesticides, fertilizers and mycotoxins.