CPA for San Diego, CA Clients: Remote Tax, Payroll and Accounting

We are a Naperville, Illinois CPA firm, and we serve San Diego County clients remotely; we have no office in California. San Diego taxes come in three layers that rarely line up: a California income tax that departs from your federal return in several places, a county property tax system with fixed calendar dates, and a city that taxes both business operators and landlords. This page covers the parts that are specific to the region. Our California page covers the statewide rules.

Where California departs from your federal return

For tax year 2025, the Franchise Tax Board (FTB) tells filers that California law in general does not conform to the One Big Beautiful Bill Act, so a figure that changed on your federal return may need an adjustment on Schedule CA. Some older gaps matter just as much:

• HSAs. Federal law lets you deduct health savings account contributions. California does not. Employer contributions shown in box 12 of your W-2 with code W are added back to California income.
• Mortgage debt. California does not follow the federal $750,000 limit on home mortgage acquisition debt, so your California itemized deduction can differ from your federal one.
• Startup stock. California does not follow the federal qualified small business stock exclusion under Sections 1202 and 1045. You report the entire gain. See our QSBS guide.
• Military retirement. For tax years 2025 through 2029, qualifying taxpayers can exclude up to $20,000 of federal military retirement pay, with income limits of $125,000 ($250,000 joint or surviving spouse).

San Diego County property tax: the dates that matter

Secured bills go out in late September. The first installment is due November 1 and becomes late after December 10, with a 10 percent penalty. The second is due February 1 and becomes late after April 10, with a 10 percent penalty plus a $10 cost. The Treasurer-Tax Collector collects more than $9.1 billion in county, city, school and special district taxes and keeps files on nearly 1 million parcels.

• Homeowners' exemption. It removes $7,000 from assessed value, worth about $70 a year. File once with the Assessor. A claim filed by February 15 gets the full benefit; one filed from February 16 through December 10 gets 80 percent, and the exemption cannot be granted for prior years. It cannot be combined with the Disabled Veterans' exemption, valued at about $1,700.
• Appeals. The Clerk of the Board says the 2026 regular filing season runs from July 2 through November 30, and applications can be filed online. Appeals of a supplemental assessment must be filed within 60 days of the mailing date on the supplemental tax bill. The Assessor also offers a free informal review.
• Proposition 19. Owners 55 or older and severely disabled owners can move their taxable value to a replacement home anywhere in California, up to three times, if it is bought or built within two years of the sale. Victims of wildfires and other declared disasters have a separate version of this transfer. A pricier home is allowed, with the excess over 100, 105 or 110 percent of the old home's value (depending on timing) added. The parent-child exclusion now covers only a family home or farm, with a $1 million figure of $1,044,586 for transfers from February 16, 2025 through February 15, 2027, per the Board of Equalization.

City of San Diego business and rental taxes

The city's Business Tax Certificate is $34 a year for 12 or fewer employees and $125 plus $5 per employee for 13 or more. Add the $4 state-mandated fee and, since July 1, 2025, a $1.47 per-employee Minimum Wage Enforcement Fee for employees working in the city. The tax is due within 15 days of starting business. A late payment costs $25 or 10 percent, whichever is greater, then 1 percent a month, and the Treasurer can bill back three years.

Landlords owe a separate Rental Unit Business Tax. For a single-family home or condominium it is a $50 base fee plus $5 per unit, generally due March 1. If no bill arrives by February 1, contact the Treasurer. The homeowners' exemption does not remove this bill.

Biotech, wireless and other employees

People at biotech and wireless companies may be paid in stock through restricted stock units or employee stock purchase plans. Our guide to ISOs, NSOs and RSUs and equity planning work cover the planning; the California-specific points are the QSBS and HSA differences above.

Tax propositions still pending on November 3, 2026

California's official voter guide lists several tax measures, and none is settled until votes are counted. Proposition 3 would make permanent the existing tax rates on income above about $371,000 for single filers (a 2025 figure, adjusted annually for inflation) instead of letting them expire in 2031. Proposition 40 would impose a one-time tax of up to 5% on certain taxpayers with covered assets valued over $1 billion. Treat both as pending when you plan.

The Indian-American community and US-India tax in San Diego

The San Diego-Chula Vista-Carlsbad metro area, which is San Diego County, has about 53,000 residents who identify as Asian Indian alone or in combination (about 1.6% of the population). The city of San Diego has about 36,000 (about 2.6%), according to the American Community Survey 2020 to 2024 5-year, Table B02018.

The consulates' 2025 jurisdiction table lists San Diego County under Los Angeles, which also covers Arizona, Nevada and New Mexico. The same table says the San Francisco consulate provides only passport services for that jurisdiction until further notice, so check which office handles your request.

Four issues come up often:

• Indian accounts. NRE and NRO balances may need reporting; see FBAR and NRE/NRO accounts.
• Indian tax paid. California does not allow a deduction for foreign income taxes, so Indian tax paid needs separate treatment on the federal foreign tax credit and on your California return.
• Mutual funds. Many Indian funds are PFICs for U.S. purposes.
• Selling property in India. California taxes long-term gains as ordinary income with no special rate; see selling property in India.

How we can help

From Naperville, we prepare federal and California returns, including Schedule CA adjustments, run payroll, keep books, review IRS and Franchise Tax Board notices, and handle US-India tax. You send documents electronically and we talk by phone or video. If a matter needs a license in California or a local professional, we will say so. This page is general information.

Frequently asked questions

General information only, not tax, legal or accounting advice for your situation. Rules, limits and deadlines change; confirm the current rules with the official source or a qualified professional before you act. Reading this page does not create a professional relationship with CPA Tax Payroll and Accounting Corp.