Many physical implementations of qubits-including ion traps, optical lattices and linear optics-suffer from loss. A nonzero probability of irretrievably losing a qubit can be a substantial obstacle to fault-tolerant methods of processing quantum information, requiring new techniques to safeguard against loss that introduce an additional overhead that depends upon the loss rate. Here we present a scalable and platform-independent protocol for estimating the average loss rate (averaged over all input states) resulting from an arbitrary Markovian noise process, as well as an independent estimate of detector efficiency. Moreover, we show that our protocol gives an additional constraint on estimated parameters from randomized benchmarking that improves the reliability of the estimated error rate and provides a new indicator for non-Markovian signatures in the experimental data. We also derive a bound for the state-dependent loss rate in terms of the average loss rate.