We develop randomized matrix-free algorithms for estimating partial traces, a generalization of the trace arising in quantum physics and chemistry. Our algorithm improves on the typicality-based approach used in [T. Chen and Y-C. Cheng, \emph{Numerical computation of the equilibrium-reduced density matrix for strongly coupled open quantum systems}, J. Chem. Phys. 157, 064106 (2022)] by deflating important subspaces (e.g. corresponding to the low-energy eigenstates) explicitly. This results in a significant variance reduction, leading to several order-of-magnitude speedups over the previous state of the art. We then apply our algorithm to study the thermodynamics of several Heisenberg spin systems, particularly the entanglement spectrum and ergotropy.
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