Accurate prediction of application performance is critical for enabling effective scheduling and resource management in resource-constrained dynamic edge environments. However, achieving predictable performance in such environments remains challenging due to the co-location of multiple applications and the node heterogeneity. To address this, we propose a methodology that automatically builds and assesses various performance predictors. This approach prioritizes both accuracy and inference time to identify the most efficient model. Our predictors achieve up to 90% accuracy while maintaining an inference time of less than 1% of the Round Trip Time. These predictors are trained on the historical state of the most correlated monitoring metrics to application performance and evaluated across multiple servers in dynamic co-location scenarios. As usecase we consider electron microscopy (EM) workflows, which have stringent real-time demands and diverse resource requirements. Our findings emphasize the need for a systematic methodology that selects server-specific predictors by jointly optimizing accuracy and inference latency in dynamic co-location scenarios. Integrating such predictors into edge environments can improve resource utilization and result in predictable performance.