Proper waste sorting is crucial for biodegradable plastics (BDPs) recycling, whose global production is increasing dynamically. BDPs can be sorted using near-infrared (NIR) sorting, but little research is available about the effect of surface contamination on their NIR spectrum, which affects their sortability. As BDPs are often heavily contaminated with food waste, understanding the effect of surface contamination is necessary. This paper reports on a study on the influence of artificially induced surface contamination using food waste and contamination from packaging waste, biowaste, and residual waste on the BDP spectra. In artificially contaminated samples, the absorption bands (ADs) changed due to the presence of moisture (1352–1424 nm) and fatty acids (1223 nm). In real-world contaminated samples, biowaste samples were most affected by contamination followed by residual waste, both having altered ADs at 1352–1424 nm (moisture). The packaging waste-contaminated sample spectra closely followed those of clean and washed samples, with a change in the intensity of ADs. Accordingly, two approaches could be followed in sorting: (i) affected wavelength ranges could be omitted, or (ii) contaminated samples could be used for optimizing the NIR database. Thus, surface contamination affected the spectra, and knowing the wavelength ranges containing this effect could be used to optimize the NIR database and improve BDP sorting.