Gravitational lensing magnification alters the observed spatial distribution of galaxies and must be accounted for to prevent biases in cosmological probes of the large-scale structure. We investigate its effects on the Dark Energy Survey year 6 galaxy clustering and galaxy-galaxy lensing analyses using the fiducial lens (position tracer) sample MagLim++. The combination of these two probes is referred to as the 2×2pt analysis, while the full 3×2pt analysis additionally includes cosmic shear. Magnification bias is parametrized by a coefficient that describes the response of the number of selected objects per unlensed area element to a change in the lensing convergence. We quantify this coefficient using the BALROG synthetic source injection catalog to account for the complexity of the selection function and compare these results with simplified estimates. The resulting values of the magnification coefficients for each redshift bin are [3.16±0.08,2.76±0.21,4.09±0.15,4.42±0.16,4.90±0.29,4.83±0.25]. Relative to year 3, this analysis provides more precise and accurate magnification bias estimates through a larger BALROG area and reweighting to better match the data properties. The cosmological results are robust when tested against various magnification parameter prior choices and also when adding cross-clustering between lens redshift bins. Neglecting magnification, however, introduces significant systematic shifts: relative to the fiducial analysis with Gaussian priors centered on the BALROG-derived estimates, we observe shifts of 1.37σ in S8 and -0.84σ in Ωm when fitting 2×2pt (which are reduced to -0.61σ in S8 and -0.71σ in Ωm for 3×2pt). This agrees with findings from simulated data, demonstrating that magnification must be modeled to avoid biases. Freeing the magnification bias in lens bin 2 leads to unphysical negative values, further justifying its exclusion from the fiducial year 6 analysis.