We present an alternative calibration of the MagLim lens sample redshift distributions from the Dark Energy Survey (DES) first three years of data (Y3). The new calibration is based on a combination of a Self-Organising Maps based scheme and clustering redshifts to estimate redshift distributions and inherent uncertainties, which is expected to be more accurate than the original DES Y3 redshift calibration of the lens sample. We describe in detail the methodology, we validate it on simulations and discuss the main effects dominating our error budget. The new calibration is in fair agreement with the fiducial DES Y3 redshift distributions calibration, with only mild differences ($<3σ$) in the means and widths of the distributions. We study the impact of this new calibration on cosmological constraints, analysing DES Y3 galaxy clustering and galaxy-galaxy lensing measurements, assuming a $Λ$CDM cosmology. We obtain $Ω_{\rm m} = 0.30± 0.04$, $σ_8 = 0.81± 0.07 $ and $S_8 = 0.81± 0.04$, which implies a $∼ 0.4σ$ shift in the $Ω_{\rm}-S_8$ plane compared to the fiducial DES Y3 results, highlighting the importance of the redshift calibration of the lens sample in multi-probe cosmological analyses.