Wavelength-dependent atmospheric effects impact photometric supernova flux measurements for ground-based observations. We present corrections on supernova flux measurements from the Dark Energy Survey Supernova Program's 5YR sample (DES-SN5YR) for differential chromatic refraction (DCR) and wavelength-dependent seeing, and we show their impact on the cosmological parameters $w$ and $Ω_m$. We use $g-i$ colors of Type Ia supernovae (SNe Ia) to quantify astrometric offsets caused by DCR and simulate point spread functions (PSFs) using the GalSIM package to predict the shapes of the PSFs with DCR and wavelength-dependent seeing. We calculate the magnitude corrections and apply them to the magnitudes computed by the DES-SN5YR photometric pipeline. We find that for the DES-SN5YR analysis, not accounting for the astrometric offsets and changes in the PSF shape cause an average bias of $+0.2$ mmag and $-0.3$ mmag respectively, with standard deviations of $0.7$ mmag and $2.7$ mmag across all DES observing bands (\textit{griz}) throughout all redshifts. When the DCR and seeing effects are not accounted for, we find that $w$ and $Ω_m$ are lower by less than $0.004±0.02$ and $0.001±0.01$ respectively, with $0.02$ and $0.01$ being the $1σ$ statistical uncertainties. Although we find that these biases do not limit the constraints of the DES-SN5YR sample, future surveys with much higher statistics, lower systematics, and especially those that observe in the $u$ band will require these corrections as wavelength-dependent atmospheric effects are larger at shorter wavelengths. We also discuss limitations of our method and how they can be better accounted for in future surveys.