The aim of this study is to implement a method to remove ambient noise in biomedical sounds captured in auscultation. We propose an incremental approach based on multichannel non-negative matrix partial co-factorization (NMPCF) for ambient denoising focusing on high noisy environment with a Signal-to-Noise Ratio (SNR) <= -5 dB. The first contribution applies NMPCF assuming that ambient noise can be modelled as repetitive sound events simultaneously found in two single-channel inputs captured by means of different recording devices. The second contribution proposes an incremental algorithm, based on the previous multichannel NMPCF, that refines the estimated biomedical spectrogram throughout a set of incremental stages by eliminating most of the ambient noise that was not removed in the previous stage at the expense of preserving most of the biomedical spectral content. The ambient denoising performance of the proposed method, compared to some of the most relevant state-of-the-art methods, has been evaluated using a set of recordings composed of biomedical sounds mixed with ambient noise that typically surrounds a medical consultation room to simulate high noisy environments with a SNR from -20 dB to -5 dB. Experimental results report that: (i) the performance drop suffered by the proposed method is lower compared to MSS and NLMS; (ii) unlike what happens with MSS and NLMS, the proposed method shows a stable trend of the average SDR and SIR results regardless of the type of ambient noise and the SNR level evaluated; and (iii) a remarkable advantage is the high robustness of the estimated biomedical sounds when the two single-channel inputs suffer from a delay between them.