Short answer

Yes. A resignation—whether tendered before, during, or after an administrative/disciplinary hearing—does not forfeit an employee’s right to receive all wages and monetary benefits already earned and clearly due, subject only to lawful deductions. What may change (or vanish entirely) are discretionary items like separation pay (generally not due in resignations) or certain bonuses conditioned on being “actively employed” on a cut-off date.

Below is a complete, Philippine-specific guide.

Legal anchors and baseline rules

Final pay is mandatory. Employers must pay all amounts already earned up to the last day of work. “Wages” are protected; withholding as a form of punishment is not allowed.
Timing of release. The Department of Labor and Employment (DOLE) has instructed that final pay be released within 30 calendar days from date of separation (sooner if company policy/CBA provides). A Certificate of Employment (COE) must be issued within three (3) days from request.
Resignation vs. dismissal.
- Resignation (Article on termination by employee) generally requires a 30-day notice unless waived by the employer. It does not entitle the employee to separation pay, unless a law, CBA, contract, or company policy says otherwise.
- Dismissal for just cause cuts off tenure immediately and carries no separation pay, but the worker is still entitled to everything already earned (e.g., unpaid wages, pro-rated 13th month, accrued SIL conversion).
Due process and hearings. The “twin-notice” and hearing requirements apply to dismissals and disciplinary sanctions. A hearing that does not result in dismissal does not wipe out earned pay. If the hearing culminates in dismissal, the employee still gets all earned and legally mandated items up to the effectivity of dismissal.

What exactly is in “final pay”?

Final pay is an umbrella term. Depending on facts, it typically includes:

Unpaid basic salary up to the last day worked (including overtime/night differential/holiday pay already earned).
Pro-rated 13th-month pay (January 1 up to separation date).
Cash conversion of unused Service Incentive Leave (SIL)—up to five (5) days minimum if the employee earned SIL and didn’t use it; some companies grant higher leave conversions by policy/CBA.
Earned, non-forfeited differentials/allowances (e.g., COLA, travel reimbursements approved per policy).
Tax refund for over-withheld income tax, if any (processed in the year-end/exit payroll).
Contractual/Policy-based bonuses that are vested or earned under the plan rules. (If a bonus requires being “employed on payout date,” it can lawfully be excluded unless already vested.)
Separation pay – not due for resignations and not due for just cause dismissals; may be due if the exit is for authorized causes (redundancy, retrenchment, closure not due to serious losses, etc.) or if granted by contract/CBA/past practice.

Key principle: If it’s earned, law-mandated, or vested by policy/contract, it belongs in final pay.

Can an ongoing disciplinary case change entitlements?

A. Employee resigns before the hearing concludes

The employer may continue or discontinue the admin case.
Final pay remains due, subject to lawful deductions (see below).
If misconduct is serious and the employer wants a dismissal finding on record (for example, to justify certain offsets or deny a discretionary bonus), the employer can complete the process for record purposes. The result may affect non-mandated pay items but not the release of earned wages.

B. Hearing finishes with a suspension or warning

The worker still resigned; the sanction doesn’t erase earned pay.
Final pay is due. Any suspension days already served are simply unpaid per penalty; other earned items remain payable.

C. Hearing finishes with dismissal for just cause effective before the intended resignation date

The mode of exit becomes dismissal.
The employee still gets earned wages, pro-rated 13th-month, SIL conversion, and any vested amounts up to the dismissal date, but no separation pay (unless policy grants it even for just-cause cases—rare).

Can the company “hold” final pay because assets weren’t returned?

Employers may implement a clearance process to confirm return of property and settlement of accountabilities.
However, they cannot indefinitely withhold all wages as a penalty. Instead, they may:
- Charge the value of unreturned or damaged property against final pay only if:
  1. there is clear proof of loss or damage;
  2. the employee was given a chance to be heard; and
  3. the deduction is lawful (see next section).
- Pursue civil/criminal remedies for shortages that exceed what can be lawfully deducted.

Practical best practice: Release the undisputed portion of final pay within the 30-day window, and document any specific offsets with basis and computation.

Lawful deductions: what can be offset from final pay?

Deductions from wages are generally prohibited unless allowed by law, regulation, or with the employee’s written authorization for a valid purpose. Commonly permitted items:

Statutory: SSS, PhilHealth, Pag-IBIG, and tax.
Company-sanctioned with written consent: salary loans, cooperative loans, company equipment purchases.
Loss or damage due to the employee’s fault or negligence, after due process, and with clear proof and valuation. (Many companies also observe the customary ≤20% cap of the employee’s wages per payroll period for such deductions; if final pay won’t recur, ensure the deduction is reasonable and well-supported to avoid an illegal deduction claim.)

What can’t be deducted: fines/penalties not authorized by law, blanket forfeiture of earned wages, or speculative/unproven losses.

Resignation during a pending case vs. “condonation” or “forgiveness”

Accepting a resignation does not automatically “forgive” an infraction. Employers may still complete the fact-finding for internal records (e.g., for reporting to regulators/clients if required). But as far as final pay is concerned, earned statutory/vested items remain payable.

Clearance, COE, and quitclaims

Clearance: Reasonable and time-bound. It should not be used to defeat the 30-day release rule.
COE: Must be issued within three (3) days from request and state dates/positions (and optionally, pay and reason for separation, if requested).
Quitclaim/Release: Often asked upon exit. It is valid only if voluntary, supported by reasonable consideration, and free from fraud/duress. A quitclaim cannot waive statutory benefits (e.g., 13th-month, SIL conversion). If the amount is unconscionably low, it may be invalidated later.

Practical timelines & workflow (for HR and employees)

Effectivity
- Employee gives 30-day notice (unless waived by employer). Agree on last day in writing.
Admin case (if any)
- Proceed with due process. Record findings and effectivity date of any sanction. If dismissal precedes the tendered resignation date, memorialize that the mode of exit is dismissal.
Compute final pay (target completion quickly; release within 30 calendar days of separation):
- Unpaid salary (including OT/ND/holiday differentials).
- Pro-rated 13th month.
- SIL conversion (up to minimum 5 days if applicable).
- Reimbursements and vested benefits.
- Lawful deductions with documentation (statutory; authorized loans; proven losses).
- Tax recomputation and any refund.
Property/Accountabilities
- Get return receipts; if loss/damage is found, issue a notice with computation and allow a response before any offset.
COE
- Prepare and issue within 3 days of request.
Release
- Pay via the regular payroll channel if possible; give a detailed pay breakdown.
- If using a quitclaim, ensure it’s voluntary and the amounts are fair and complete.

Frequently asked questions

1) If the resignation was “effective immediately,” can the company deduct 30 days’ pay? No. There is no legal “liquidated damages” for failing to render the 30-day notice unless a valid contract explicitly provides a reasonable penalty. The usual remedy is for the employer to accept the shortened notice (expressly or impliedly) or to hold the employee liable for provable damages—not to forfeit earned wages.

2) Is a performance bonus payable after resignation? It depends on the plan rules. If the plan says the employee must be active on payout date and the employer consistently enforces that, it may be excluded. If the plan vests pro-rata on separation, include it.

3) What if the hearing proves theft and the item’s value exceeds final pay? The employer may offset the proven value (after due process) up to the final pay amount and then pursue civil/criminal remedies for the excess. Document everything.

4) Can final pay be released only after clearance is fully completed? Clearance may sequence approvals, but it cannot justify indefinite withholding. At minimum, release the undisputed portion within 30 days.

5) Are resigning probationary employees treated differently? Not for final pay: they still receive earned wages, pro-rated 13th month, and SIL conversion (if they earned SIL/are covered). Separation pay rules are the same (generally none for resignation).

Sample final pay checklist (employer)

Written resignation & effectivity date (or dismissal memo if applicable)
Last day worked confirmation
Payroll cut-off accruals (OT/ND/holiday)
13th-month pro-ration
SIL balance & conversion
Approved reimbursements
Loan ledgers with written authorizations
Loss/damage notice, proof, valuation, employee reply (if offsetting)
Tax recomputation / refund
COE drafting (ready within 3 days of request)
Quitclaim (optional; ensure voluntariness and fair consideration)
Release within 30 days, with payslip-style breakdown

Bottom line

Resignation doesn’t erase earned pay. Even amid or after a disciplinary hearing, the employee remains entitled to all earned and legally mandated amounts.
Withholding is limited. Only lawful, documented deductions may reduce final pay.
Process matters. Follow due process for any offsets, issue the COE promptly, and release final pay within 30 days of separation.

This article is for general information and does not replace formal legal advice. For high-stakes situations (e.g., alleged fraud, large offsets, or disputed bonuses), consult a Philippine labor law specialist.