This paper develops a stochastic programming framework for multi-agent systems where task decomposition, assignment, and scheduling problems are simultaneously optimized. Due to their inherent flexibility and robustness, multi-agent systems are applied in a growing range of real-world problems that involve heterogeneous tasks and uncertain information. Most previous works assume a unique way to decompose a task into roles that can later be assigned to the agents. This assumption is not valid for a complex task where the roles can vary and multiple decomposition structures exist. Meanwhile, it is unclear how uncertainties in task requirements and agent capabilities can be systematically quantified and optimized under a multi-agent system setting. A representation for complex tasks is proposed to avoid the non-convex task decomposition enumeration: agent capabilities are represented as a vector of random distributions, and task requirements are verified by a generalizable binary function. The conditional value at risk (CVaR) is chosen as a metric in the objective function to generate robust plans. An efficient algorithm is described to solve the model, and the whole framework is evaluated in two different practical test cases: capture-the-flag and robotic service coordination during a pandemic (e.g., . Results demonstrate that the framework is scalable, generalizable, and provides low-cost plans that ensure a high probability of success.