This paper presents a scalable approach to model uncertainties within a UAV (Unmanned Aerial Vehicle) embedded mission manager. It proposes a concurrent version of BFM models, which are Bayesian Networks built from FMEA (Failure Mode and Effects Analysis) and used by MDPs (Markov Decision Processes). The models can separately handle different applications during the mission; they consider the context of the mission including external constraints (luminosity, climate, etc.), the health of the UAV (Energy, Sensor) as well as the computing resource availability including CPU (Central Processing Unit) load, FPGA (Field Programmable Gate Array) use and timing performances. The proposed solution integrates the constraints into a mission specification by means of FMEA tables in order to facilitate their specifications by non-experts. Decision-making processes are elaborated following a “just enough” quality management by automatically providing adequate implementation of the embedded applications in order to achieve the mission goals, in the context given by the sensors and the on-board monitors. We illustrate the concurrent BFM approach with a case study of a typical tracking UAV mission. This case also considers a FPGA-SoC (FPGA-System on Chip) platform into consideration and demonstrates the benefits to tune the quality of the embedded applications according to the environmental context.