When acquired at short echo-time, the proton MRS signals contain contributions from metabolites and water, and a large baseline (‘background’) component. The background contributions in proton short echo-time MRS signals make accurate and reliable quantification difficult. The purpose of the present study was to compare the influence of the background-accommodation strategy on the metabolite concentration estimates at 7 T using QUEST. Two strategies were investigated to accommodate the background, (1) the measured background signal was incorporated in the metabolite basis-set; and (2) the background signal was estimated and subtracted from the in vivo signal using Subtract-QUEST. The influence of the background-accommodation strategy was addressed with the aid of Monte Carlo and in vivo studies. For the signals considered in this study, statistically significant differences between the in vivo concentration estimates using the two approaches were observed for three metabolites namely Cho, NAA, and Tau. The observed underestimation of the ‘background’ estimates using Subtract-QUEST led to an overestimation of these metabolite estimates. Consequently, we can conclude that, including the ‘background’ signal in the metabolite basis-set would lead to more accurate quantifications at higher magnetic field strengths when the differences between the apparent relaxation times of the ‘background’ and the metabolite signals are reduced. However, the use of the Subtract-QUEST method is the method of choice when measurement time is critical especially for diseased animals.