Southampton
Nonprofit accounting in Southampton, NY
With the largest year round population on the East End, Southampton has the most service delivery nonprofits we see.
What you get
- Form 990, 990-EZ and 990-N
- Unrelated business income on Form 990-T
- Restricted and unrestricted funds tracked
- Reporting a board can read

The MyCleverCPA team
- 25+ years in regulated finance, compliance and audit
- Tax work led by a CPA. Jillian Sinel holds the CPA and the CAA
- Hamptons Office at 30 Lincoln St, Sag Harbor, NY 11963
In Southampton
Nonprofit accounting for Southampton
Real payroll, real programs and cost allocation across program, administration and fundraising that has to be defensible rather than convenient. The ratios on the return get read.
Organizations working alongside the hospital and the schools also tend to have government or foundation money, which brings its own reporting on top of the 990.
Scope
What is included in nonprofit
The same work wherever you are. Scoped to what you actually need.
Annual filings
- Form 990, 990-EZ and 990-N
- Form 990-T for unrelated business income
- New York State charities filings
Fund accounting
- Restricted and unrestricted fund tracking
- Grant and program reporting
- Costs allocated across program, administration and fundraising
Governance and controls
- Internal controls for volunteer-run finance
- Separation of duties on a small team
- Documentation a board can actually review
Setting one up
- Entity formation and the exemption application
- A chart of accounts built to produce a 990
- The written policies the 990 asks whether you have
What this covers
- Form 990, 990-EZ and 990-N
- Form 990-T for unrelated business income
- Annual reporting and regulatory filings
- Nonprofit structuring and entity setup
- Bookkeeping and fund accounting
- Board and management reporting
- Restricted and unrestricted fund tracking
- Internal controls for volunteer-run finance
Local tax
A permit for every rental, and the U.S. Open question
Southampton town requires a rental permit for any home rented for any period, with a 14 day minimum stay. Anything shorter is a prohibited transient rental. Permits last two years and are not transferable, which means a buyer of a rental house needs their own permit rather than inheriting the seller’s. That one catches people at closing. Advertising, listing or showing a house for rent without a permit in place can bring violations, suspension and a two year rental restriction. Processing takes roughly one to three weeks off season and two to four in summer, so it is not a last minute item.
The 2026 U.S. Open at Shinnecock Hills in June is the live local question. Southampton moved to temporarily relax its short term rental limits for the event, and neighboring Sagaponack waived its two week minimum for 12 to 23 June. Both of those rest on local reporting rather than on a code section we can point you to, so confirm the adopted resolution with the Town before you let anything.
The tax side is clearer. If you rent your home for 14 days or fewer in the year and you use it as a residence, the income can be excluded entirely under the section 280A rule, though no expenses are then deductible. At 15 days it becomes reportable rental activity with allocation between personal and rental use. For a single championship week, that distinction is usually the whole conversation.
The Peconic transfer tax applies at 2.5% across the town with the $400,000 improved residential allowance, again only where consideration is $2,000,000 or less. Zone 2 for MCTMT at 0.34%.
How it works
How nonprofit runs
Four stages. Most of the value sits in the first two, before anything is filed.
Check the filing history
Which 990 was filed, when, and whether exempt status is still intact.
Straighten the records
Funds separated, allocations documented and balances reconciled.
Prepare the return
The 990 and anything it brings with it, including the 990-T.
Report to the board
Statements and a 990 the board can read without a translator.
Questions
Frequently asked questions
I want to rent my house for U.S. Open week. What do I need to know?
Two things. Whether the permit rules allow it, which the town moved to relax temporarily for the event but which you should confirm directly with the Town before committing. And the tax treatment: at 14 days or fewer the income can be excluded entirely, at 15 days it is reportable rental activity. For one week, that usually means it is excludable, but the permit question is separate and comes first.
I just bought a rental house. Does the seller’s permit carry over?
No. Southampton rental permits are not transferable, so a new owner needs their own before renting or even advertising. Allow two to four weeks in summer.
Do you work with the trades out here?
Yes, and it is a large part of this office. Worker classification between 1099 and W-2, seasonal payroll, equipment depreciation and the sales tax treatment of capital improvements are the four that come up every year.
Do you work in Spanish?
Tell us what you need when you book and we will arrange the meeting accordingly.
What happens if we missed a 990?
Three consecutive missed years revokes exempt status automatically. One missed year is fixable and worth fixing immediately. If status has already been revoked, reinstatement is possible but it is a longer road.
Which 990 do we file?
It depends on gross receipts and total assets. Small organizations may only need the 990-N, which is short. We would rather confirm the threshold than have you file the wrong one.
Can you help us set up a new nonprofit?
Yes, on the structuring and accounting side, working with whoever handles the legal formation and the exemption application.
Also in Southampton
Our other services here
Tax preparation and planning
Southampton returns split two ways, because the town has a real year round economy alongside the second home money.
Tax preparation and planning in SouthamptonBookkeeping and accounting
Contractors, landscapers and property managers make up most of the bookkeeping work here.
Bookkeeping and accounting in SouthamptonTrust and estate tax
Southampton estates often include both a residence and income property.
Trust and estate tax in SouthamptonIRS representation
Contractor notices here are usually about worker classification.
IRS representation in SouthamptonTalk to us about nonprofit in Southampton
Book a time online, or call the Hamptons office directly.
Nearest office
Hamptons Office
30 Lincoln St, Sag Harbor, NY 11963
Phone
Office hours
Sunday to Friday, 11am to 8pm Eastern.
Closed Saturday.