A computer-implemented method for inferring genetic ancestry from low-coverage genomic data may include (i) generating a reference matrix representing a genetic reference panel in terms of dosages for given reference samples at given loci, (ii) decomposing the reference matrix via non-negative matrix factorization into an ancestral genotype matrix and an ancestral attribution matrix, (iii) resampling the reference matrix, (iv) deriving an ancestral alternate reads matrix that, when multiplied with the ancestral attribution matrix, approximates the resampled reference matrix, (v) deriving an ancestral attribution vector that, when multiplied with the ancestral alternate reads matrix, approximates a vector representing the test sample, and (vi) determining the genetic ancestry of the subject based on the ancestral attribution vector. Various other methods, systems, and computer-readable media are also disclosed.