Residents of Puerto Rico are subject to federal income tax on their worldwide income. However, U.S. Code Section 933 permits a bona fide individual resident of Puerto Rico to exclude the Puerto Rico source of income from his gross income for U.S. tax purposes. The bona fide residence in Puerto Rico for income tax purposes is established through the three tests included in U.S. Code Section 937: the (a) the presence test, (b) tax home test, and (c) closer connection test. Bona fide residents of Puerto Rico will be subject to U.S. income tax on income from sources outside Puerto Rico.
Individuals resident of Puerto Rico whose gross income for the taxable year, net of exemptions, exceeds $5,000; or not resident of Puerto Rico, and citizen of the United States, whose gross income from Puerto Rico sources for the taxable year, net of exemptions, exceeds $5,000, must file a Puerto Rico income tax return.
Self-employed persons in Puerto Rico are required to pay federal FICA taxes
If you have income that is effectively connected with business in Puerto Rico, you must file a 1040PR with the IRS to report your self-employment income and, if necessary, pay self-employment tax.
Self-employed individuals must pay an estimated tax if they expect to owe at least $1,000 of Puerto Rico income tax or Federal tax, during the taxable year, after subtracting his withholdings and refundable credits.