Accurate workload prediction and throughput estimation are keys in efficient proactive power and performance management of multi-core platforms. Although hardware performance counters available on modern platforms contain important information about the application behavior, employing them efficiently is not straightforward when dealing with time-varying applications even if they have iterative structures. In this work, we propose a machine learning-based framework for workload prediction and throughput estimation using hardware events. Our framework enables throughput estimation over various available system configurations, namely, number of parallel threads and operating frequency. In particular, we first employ workload clustering and classification techniques along with Markov chains to predict the next workload for each available system configuration. Then, the predicted workload is used to estimate the next expected throughput through a machine learning-based regression model. The comparison with state of the art demonstrates that our framework is able to improve Quality of Service (QoS) by 3.4x, while consuming 15% less power thanks to the more accurate throughput estimation.