Organic-inorganic hybrid materials can introduce more flexibility in the choice of Li-ion battery materials due to the versatility of organic ligands. As an alternative to carboxylate-based ligands, Fe and Co methylene diphosphonate were successfully synthesised and tested as model diphosphonate-based negative electrode materials for Li-ion batteries, showing specific charges of 250 mAh g−1 and 395 mAh g−1 after 100 cycles at 50 mAh g−1, respectively. Operando X-ray diffraction and ex situ X-ray absorption spectroscopy confirmed the expected conversion reaction mechanism involving amorphisation of the pristine materials and extrusion of transition metal particles upon reduction. Ex situ X-ray absorption spectra indicated that Fe methylene diphosphonate undergoes reversible Fe cycling between Fe(II) and Fe(0) metal particles.