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Measurement-device-independent quantum key distribution (MDI-QKD) closes all the security loopholes in the detection system and is a promising solution for secret key sharing. Polarization encoding is the most common QKD encoding scheme, as it is straightforward to prepare and measure. However, implementing polarization encoding in MDI QKD imposes extra challenges, as polarization alignment must be maintained over both mutually unbiased bases and be maintained for both paths (Alice-Charlie and Bob-Charlie). Polarization alignment is usually done by interrupting the QKD process (reducing overall key generation rates) or using additional classical laser sources multiplexed with quantum channels for polarization alignment. Since low key rates and cost are the two most pressing challenges preventing wide adoption of QKD systems, using additional resources or reducing key rates runs contrary to making QKD commercially viable. Therefore, we propose and implement a novel polarization compensation scheme in the MDI-QKD system that avoids the aforementioned drawbacks by recycling part of discarded detection events. Our scheme evaluates the polarization drift in real-time based on single measurements corresponding to decoy intensities. Our fully automated experimental demonstration maintains the average polarization drift below 0.13 rad over 40 km of spooled fibre (without an insulating jacket) for at least four hours. The average quantum bit error rate is 3.8$\%$, and we achieved an average key rate of $7.45\times 10^{-6}$ bits per pulse.