During cheese manufacturing, on average 90% of the starter culture cells are believed to be entrapped in the curd, with the remainder lost in whey. This paper shows that plasmid-cured dairy strains of Lactococcus lactis show cell retention in the curd of 30–72%, whereas over-expression of pili on the lactococcal cell surface can increase cell retention to 99%. Exopolysaccharide production and cell clumping and chaining do not influence cell retention in cheese curd. L. lactis surface alteration also strongly affected the distribution of cells in the cheese matrix: clumping and over-expression of pili led to formation of large cell aggregates embedded in the protein matrix whereas exopolysaccharide expression resulted in cells being surrounding by small serum regions in the protein matrix of the cheese. These results suggest that surface properties of dairy starter cultures strongly determine retention and distribution of the bacteria in cheese curd.