Generative Flow Networks (GFlowNets) have demonstrated significant performance improvements for generating diverse discrete objects x given a reward function R(x), indicating the utility of the object and trained independently from the GFlowNet by supervised learning to predict a desirable property y given x. We hypothesize that this can lead to incompatibility between the inductive optimization biases in training R and in training the GFlowNet, potentially leading to worse samples and slow adaptation to changes in the distribution. In this work, we build upon recent work on jointly learning energy-based models with GFlowNets and extend it to learn the joint over multiple variables, which we call Joint Energy-Based GFlowNets (JEBGFNs), such as peptide sequences and their antimicrobial activity. Joint learning of the energy-based model, used as a reward for the GFlowNet, can resolve the issues of incompatibility since both the reward function R and the GFlowNet sampler are trained jointly. We find that this joint training or joint energy-based formulation leads to significant improvements in generating anti-microbial peptides. As the training sequences arose out of evolutionary or artificial selection for high antibiotic activity, there is structure in the distribution of sequences that reveals information about the antibiotic activity, giving an advantage to modeling their joint generatively vs. pure discriminative modeling. We also evaluate JEBGFN in an active learning setting for discovering anti-microbial peptides.