We examine the performance of a quantum phase gate implemented with cold neutral atoms in microtraps, when anharmonic traps are employed and the effects of finite temperature are also taken into account. Both the anharmonicity and the temperature are found to pose limitations to the performance of the quantum gate. We present a quantitative analysis of the problem and show that the phase gate has a high quality performance for the experimental values that are presently or in the near future achievable in the laboratory.