The Ear-ECG provides a continuous Lead I like electrocardiogram (ECG) by measuring the potential difference related to heart activity by electrodes which are embedded within earphones. However, the significant increase in wearability and comfort enabled by Ear-ECG is often accompanied by a degradation in signal quality - an obstacle that is shared by the majority of wearable technologies. We aim to resolve this issue by introducing a Deep Matched Filter (Deep-MF) for the highly accurate detection of R-peaks in wearable ECG, thus enhancing the utility of Ear-ECG in real-world scenarios. The Deep-MF consists of an encoder stage, partially initialised with an ECG template, and an R-peak classifier stage. Through its operation as a Matched Filter, the encoder searches for matches with an ECG template in the input signal, prior to filtering these matches with the subsequent convolutional layers and selecting peaks corresponding to the ground-truth ECG. The latent representation of R-peak information is then fed into a R-peak classifier, of which the output provides precise R-peak locations. The proposed Deep Matched Filter is evaluated using leave-one-subject-out cross-validation over 36 subjects with an age range of 18-75, with the Deep-MF outperforming existing algorithms for R-peak detection in noisy ECG. The Deep-MF achieves a median R-peak recall of 94.9% and a median precision of 91.2% across subjects when evaluated with leave-one-subject-out cross validation. Overall, this Deep-Match framework serves as a valuable step forward for the real-world functionality of Ear-ECG and, through its interpretable operation, the acceptance of deep learning models in e-Health.