Predicting resource usage of applications running in a virtual environment may include executing benchmarks in a native system and collecting first traces of resource utilization metrics; executing the same benchmarks in a virtual environment and collecting second traces of resource utilization metrics; generating a first prediction model that maps selected first traces to the second traces; generating a second prediction model that maps second selected first traces to the second traces; combining first and second application traces generated from running first and second applications on the native system; and predicting a combined resource usage of the first and second applications running in the virtual environment by applying the first and second prediction models to the combined application traces.