Methods utilizing instrumental variables have been a fundamental statistical approach to estimation in the presence of unmeasured confounding, usually occurring in non-randomized observational data common to fields such as economics and public health. However, such methods usually make constricting linearity and additivity assumptions that are inapplicable to the complex modeling challenges of today. The growing body of observational data being collected will necessitate flexible regression modeling while also being able to control for confounding using instrumental variables. Therefore, this article presents a nonlinear instrumental variable regression model based on Bayesian regression tree ensembles to estimate such relationships, including interactions, in the presence of confounding. One exciting application of this method is to use genetic variants as instruments, known as Mendelian randomization. Body mass index is one factor that is hypothesized to have a nonlinear relationship with cardiovascular risk factors such as blood pressure while interacting with age. Heterogeneity in patient characteristics such as age could be clinically interesting from a precision medicine perspective where individualized treatment is emphasized. We present our flexible Bayesian instrumental variable regression tree method with an example from the UK Biobank where body mass index is related to blood pressure using genetic variants as the instruments.