FSA/HSA Contributions Are Getting Deducted from Payroll, But Don't Appear in Beancount—Where Do They Go?

General
1

My paycheck shows:

  • Gross: $5,000
  • FSA: -$250
  • Health insurance: -$400
  • Net: $4,350

In Beancount, I record Gross salary + payroll taxes. But where does the FSA $250 go? It’s not in my checking account. And what’s the difference between FSA and HSA—I have both available on my plan and I’m confused.

For Beancount: should I track FSA and HSA as separate accounts? Or are they just deductions from salary (like taxes) that I ignore in Beancount?

For employees: do you track FSA/HSA at all, or let employer handle it?

2

FSA vs HSA: HSA is yours to keep forever, invest it. FSA is use-it-or-lose-it within calendar year. Which do you have?

3

FSA: employer takes it pre-tax, sits in separate account (you access via debit card or submit receipts for reimbursement). Beancount: most people don’t track FSA (employer handles it). Just treat as payroll deduction, like taxes.

HSA: this one matters. It’s YOUR account, invested, portable. I track HSA as investment account in Beancount (similar to brokerage account). Contributions are deductible, withdrawals for medical are tax-free.

For you: FSA can be ignored. HSA should be tracked if you’re investing it.

4

Two tax points: (1) FSA/HSA contributions reduce your gross income for tax purposes (employer reports on W-2). (2) HSA is triple-tax-advantaged—deductible, grows tax-free, withdraw tax-free for medical. This makes HSA a hidden retirement account (if you don’t need it for medical, keep it invested).

For Beancount modeling: FSA can be ignored. HSA should have its own account and investment tracking.