Phosphorus fertilisation is crucial for crop yields. However, traditional phosphate resources are dwindling, thus a more efficient use of phosphorus fertilisers is required for sustainable farming. This study demonstrates the scope of image-based models parameterised by elemental maps by assessing how a dynamic root system architecture may improve phosphorus root uptake from a fertiliser pellet. A multi-image based modelling method was developed by utilising structural imaging coupled with elemental maps. Structural imaging was used to capture barley (Hordeum vulgare L. cv. Optic) root, soil and fertiliser pellet configurations as a domain for numerical simulations. Elemental mapping was used to image phosphorus in soil thin-sections of the same samples. These two imaging modes were aligned using an automated method and image-based models describing the diffusion and root-uptake of phosphorus in soil were parameterised using the elemental maps. Structural imaging showed root length density was increased inside and near the fertiliser pellet. Averaging elemental data revealed phosphorus gradients from the pellet. Modelling results suggested: the pellet only enhances phosphorus uptake of roots within 2 mm over 30 days, densely packed roots decrease phosphorus uptake efficiency, and a root system that responded to nutrients from a fertiliser have comparatively increased phosphorus uptake efficiency near the pellet. The combination of structural and elemental imaging provides the means to accurately parameterise both the geometric and chemical aspects of models describing phosphorus movement in root-soil-fertiliser systems. This approach may be applicable to other plant-soil systems where structure and elemental quantities are important to the problem.