Three metal ammonium (ammonia) carbonate double salts were mechanochemically synthesized including magnesium ammonium carbonate ([NH4]2Mg[CO3]2·4H2O, MAC), copper ammonium carbonate ([NH3]2Cu(CO3), CAC), and zinc ammonium carbonate ((NH3)Zn(CO3), ZAC), and their crystallinity and thermal stability were investigated using in situ X-ray diffraction. The crystal structures were investigated in the temperature interval from 25 to 355 °C. MAC exhibited relatively low thermal stability with its crystal structure rapidly losing crystalline water as well as ammonium ions already at 85 °C and transforming into an amorphous carbonate, as confirmed by in situ infrared spectroscopy. CAC and ZAC exhibited loss of the corresponding NH3 at much higher temperatures transforming into a mixture of the corresponding metal oxides according to the XRD with the outer layer of the carbonate, as suggested by infrared spectroscopy measurements. The thermogravimetric analysis has been carried out to investigate the thermal degradation behavior. Initial fast mass loss was observed in the parent [NH4]2CO3 already under 100 °C with complex mass loss patterns from basic carbonate precursors achieving stable mass at above 500 °C for magnesium carbonate. CAC and ZAC inherited intermediate responses to temperature when compared to the precursors exhibiting stable mass at ~ 300 °C. This can be associated with the distinct crystal structure of the compounds whereby CAC and ZAC exhibit strong bonds with metal ions, while in MAC crystalline water contributes to lower stability of the crystal as well as the loosely bound ammonium ion. Infrared spectra were obtained and interpreted at room temperature followed by their in situ thermal analysis up to 250 °C in attenuated total reflection mode. Changes in the complex room temperature spectra with increasing temperature were interpreted as loss of N–H bonds, as confirmed by the concurrent decrease in the 3350–3000 and 1248 cm−1 band region. It was found that ZAC was the most thermally stable compound among the three double salts. The thermal data obtained in this work have practical implications for nutrient recovery and their release in the environment.