Model uncertainty is rarely considered in the field of biogeochemical modeling. The standard biogeochemical modeling approach is to proceed based on one selected model with the “right” complexity level based on data availability. However, other plausible models can result in dissimilar answer to the scientific question in hand using the same set of data. Relying on a single model can lead to underestimation of uncertainty associated with the results and therefore lead to unreliable conclusions. Multi-model ensemble strategy is a means to exploit the diversity of skillful predictions from different models with multiple levels of complexity. The aim of this paper is two fold, first to explore the impact of a model’s complexity level on the accuracy of the end results and second to introduce a probabilistic multi-model strategy in the context of a process-based biogeochemical model. We developed three different versions of a biogeochemical model, TOUGHREACT-N, with various complexity levels. Each one of these models was calibrated against the observed data from a tomato field in Western Sacramento County, California, and considered two different weighting sets on the objective function. This way we created a set of six ensemble members. The Bayesian Model Averaging (BMA) approach was then used to combine these ensemble members by the likelihood that an individual model is correct given the observations. Our results demonstrated that none of the models regardless of their complexity level under both weighting schemes were capable of representing all the different processes within our study field. Later we found that it is also valuable to explore BMA to assess the structural inadequacy inherent in each model. The performance of BMA expected prediction is generally superior to the individual models included in the ensemble especially when it comes to predicting gas emissions. The BMA assessed 95% uncertainty bounds bracket 90–100% of the observations. The results clearly indicate the need to consider a multi-model ensemble strategy over a single model selection in biogeochemical modeling study.