Subseries B. Shipping and Business Papers includes documents relating to more than one ship, correspondence, accounts, and insurance papers. Financial materials relating to Stephen's partners Henry Prince and Nathan Peirce (Phillips' brother-in-law) are also found in this section. Many of these papers are prices current with personal holograph notes to Phillips on the inside leaves. These papers were used as sources of current market prices for various goods in specific ports, however they also document the impacts of military action upon maritime commerce.

According to James Duncan Phillips (see bibliography), Stephen Clarendon took charge of his father's shipping business in 1821. All shipping and business papers dated previous to 1821 have been retained with the Stephen Phillips Papers, while those generated after 1820 have been included in the Stephen Clarendon Phillips Papers.