P systems provide a high level computational modelling framework that combines the structural and dynamical aspects of ecosystems in a compressive and relevant way. The inherent randomness and uncertainty in biological systems is captured by using probabilistic strategies. The design of efficient simulation algorithms in order to reproduce the behavior of these computational models over conventional computers is fundamental for the validation and virtual experimentation processes. In this paper, we describe the modelling framework and two different simulation algorithms. As a case study, a P system based model of an ideal ecosystem with three trophic levels is designed and simulated by both simulation algorithms, providing comparisons of efficiency between them.