Phillips returned stateside with the San Francisco 49ers in the fall of 1999. The 49ers interviewed him several times before seemingly being assured that he had put his past difficulties behind him, though general manager Bill Walsh told him that the 49ers would not hesitate to cut him if he stepped out of line. He was in contention for the starting job before pulling a hamstring in training camp. Additionally, his blocking left much to be desired. He was beaten out for the starting slot by Charlie Garner. He did, however, become the 49ers' primary kick returner.