The applicability of ionic liquids has grown exponentially over the last few decades. This growth is due to the easy modification of these compounds formed by ions, through the proper choice of both moieties, and the possibility of introducing functional groups into their cations and anions. However, studies of their toxicity and effects on the environment remain scarce. This study analyses firstly the response to adding different concentrations of choline dihydrogen phosphate to the germination of seeds of eight plant species. It also examines the microbial population and the respiration of two soils with contrasting organic matter contents. Seeds were incubated in a Petri dish in a Phytotron with a photoperiod of 16 h under light at 24 °C and 8 h in darkness at 16 °C. The activity of microbial populations of untreated and treated soils was analysed by isothermal microcalorimetry at 25 °C. Basal soil respiration kinetics were measured at optimal moisture (80% of field water retention capacity) and temperature (25 °C) over 10 days. The results indicate that this compound has diverse effects on the different endpoints. Nevertheless, this compound can be classified as non-toxic considering its effects on seeds and on soil, at least in the medium- to long-term.