Economic evaluations from individual level data are an important component of the process of technology appraisal, with a view to informing resource allocation decisions. A critical problem in these analyses is that both effectiveness and cost data typically present some complexity (eg, nonnormality, spikes, and missingness) that should be addressed using appropriate methods. However, in routine analyses, standardised approaches are typically used, possibly leading to biassed inferences. We present a general Bayesian framework that can handle the complexity. We show the benefits of using our approach with a motivating example, the MenSS trial, for which there are spikes at one in the effectiveness and missingness in both outcomes. We contrast a set of increasingly complex models and perform sensitivity analysis to assess the robustness of the conclusions to a range of plausible missingness assumptions. We demonstrate the flexibility of our approach with a second example, the PBS trial, and extend the framework to accommodate the characteristics of the data in this study. This paper highlights the importance of adopting a comprehensive modelling approach to economic evaluations and the strategic advantages of building these complex models within a Bayesian framework.