The development and application of artificial intelligence-based computer vision systems in medicine, environment, and industry are playing an increasingly prominent role. Hence, the need for optimal and efficient hyperparameter tuning strategies is more than crucial to deliver the highest performance of the deep learning networks in large and demanding datasets. In our study, we have developed and evaluated a new training methodology named deep multi-metric training (DMMT) for enhanced training performance. The DMMT delivers a state of robust learning for deep networks using a new important criterion of multi-metric performance evaluation. We have tested the DMMT methodology in multi-class (three, four, and ten), multi-vendors (different X-ray imaging devices), and multi-size (large, medium, and small) datasets. The validity of the DMMT methodology has been tested in three different classification problems: (i) medical disease classification, (ii) environmental classification, and (iii) ecological classification. For disease classification, we have used two large COVID-19 chest X-rays datasets, namely the BIMCV COVID-19+ and Sheffield hospital datasets. The environmental application is related to the classification of weather images in cloudy, rainy, shine or sunrise conditions. The ecological classification task involves a classification of three animal species (cat, dog, wild) and a classification of ten animals and transportation vehicles categories (CIFAR-10). We have used state-of-the-art networks of DenseNet-121, ResNet-50, VGG-16, VGG-19, and DenResCov-19 (DenRes-131) to verify that our novel methodology is applicable in a variety of different deep learning networks. To the best of our knowledge, this is the first work that proposes a training methodology to deliver robust learning, over a variety of deep learning networks and multi-field classification problems.