Research into seed germination classroom activities has been common in the last few decades. Didactic proposals have generally focused on the implementation of guided activities in a specific educational stage and context, and an evaluation of the results. However, it is not evident that students approach seed and germination concepts with a reasoned argument. In light of this, comparative research using an inquiry approach was undertaken with 59 primary school students and 82 trainee teachers at an education faculty in Spain, over two academic years. The results showed that it is necessary to give greater relevance to experimental activities to produce reasoned argumentation of seed and germination concepts. Activities should focus on variables that differ from those typical of common or historical agricultural knowledge. Variables derived from genetic information (size of the seed, latency period) are significant and helpful. It is also considered essential to work on the meaning and proper use of scientific terms, such as living and inert matter, sun-light-heat, or plant germination and growth processes. The search for explanations and the development of justifications, for example relating the excess of water to a lack of oxygen for the seeds, is also essential.