Changes in magnetic and chemical properties of soil during the growth of tomato plants (Lycopersicon esculentum) are examined in this study. The synthetic soils, prepared from sand, topsoil and organic material, were treated with magnetite powder (<5 μm) in order to simulate metal contamination. Six soil treatments were prepared from two soil types: controls, low-contamination and high-contamination treatments (0.01 and 0.05 g of magnetite powder/kg soil, respectively). Overall, the contaminated soils had a greater decrease in magnetic susceptibility (MS) than the controls, and the difference in MS decrease between the treatments was found to be statistically significant for both soil types. Potential reasons for the overall MS decrease were explored, and among them, trace element uptake by plants probably had a minor contribution as the concentration differences of Fe and other trace elements (Ni, Mn) between treatments were not statistically significant. In soils, oxidized and weakly magnetic minerals (maghemite, goethite and hematite) were common after plant growth, when compared with the untreated (background) soil. Such mineral transformations could have contributed to the overall MS decrease. The results show that exposure to Fe contaminants can affect plant growth and suggest that plant growth can measurably change the magnetic properties of their growth media. While the potential variables affecting plant growth were controlled as much as possible, there still remains the potential that biotic and abiotic chemical reactions could have affected the results. Thus, continuous monitoring of the changes in soil magnetic and chemical properties in more complex soil–plant systems is needed.