Various technologies have been implemented in wastewater treatment plants (WWTPs) to generate clean effluent with minimised impacts on the environment. Thermal hydrolysis process (THP) and struvite crystallisation reactors are two examples of these technologies. THP generates humic-like substances, known as melanoidins, that are presumed to disrupt struvite crystallisation. THP also solubilises trace elements that are prone to complex with melanoidins. On the one hand, the trace elements might stay bound to the melanoidins in the supernatant or on the other hand; they might be present in struvite as impurities. As both THP and struvite crystallisation are promising technologies, the objective of this study was to understand the effects of THP on struvite crystallisation. Results showed that melanoidins generated by THP affected P removal and the amount of produced struvite in struvite crystallisation at pH 6.5 and 7.25, but not at pH 8. In contrary to melanoidins, humic acids (HA) were found to reduce P removal efficiency at pH 8. Melanoidins resulted in slightly higher N-NH4 concentration in the supernatant in all pH values. Melanoidins and HA also changed crystal colour from white into brown and black, respectively. Furthermore, melanoidins and HA changed the morphology of struvite crystals from X-shaped and long rod-like crystals into square-shaped crystals and at the same time reduced the diameter of struvite crystal. Regardless, melanoidins did not change the Mg:N-NH4:P-PO4 molar ratio. Melanoidins did not significantly influence induction time, except at pH 7.25 and 2 g TOC/L melanoidins. In addition to this, melanoidins were found to form complexes with magnesium which subsequently decreased the supersaturation and affected struvite crystallisation. Different elements had different fate on struvite crystallisation. Melanoidins formed complexes with Mn and Ni, resulting in a higher concentration in the supernatant compared to the condition without melanoidins. Based on PHREEQC modelling, humic substances (HS) formed complexes with Ca, Cu, and Fe. Certain trace elements (Ca, Co, Cu, Fe, and Mn) and heavy metals (Al and Cr) were found to co-precipitate with struvite in all experimental conditions; meanwhile, Se minerals only co-precipitated at pH 8. All minerals showed decreasing SI with increasing HS concentrations. The decrease of SI implied that there would be less co-precipitation of Al, Ca, Co, Cr, Cu, Fe, Mn, and Se in struvite crystals. Nevertheless, their presence in the supernatant would not guarantee the bioavailability of the trace elements for bacteria in partial nitritation/anammox (PN/A) processes due to the chance of complexation with HS. Eventually, it could be concluded that THP affected struvite crystallisation and Response Surface Methodology (RSM) confirmed that the optimum conditions for struvite crystallisation with maximised N and P contents and big diameter were pH of 7.9 and 0 g TOC/L melanoidins. Nonetheless, melanoidins prevented co-precipitation of trace elements in struvite crystals.