Here’s a comprehensive, plain-English legal article (Philippine context) on Clearance Processing Delays After Resignation—what employers can and can’t do, timelines, what “clearance” actually covers, and the practical steps to get your last pay and documents. This is general information, not legal advice. Facts, your contract/CBA, and company policies matter.

1) Big picture

“Clearance” is an internal process to confirm you’ve returned company property, settled cash/asset accountabilities, and finished handover.
Your legal rights (final pay, 13th month, leave conversion, tax forms, COE) don’t disappear because clearance is slow. Employers may verify accountabilities, but they can’t stall indefinitely or set conditions that contradict labor rules.

Key timelines you should know

Final pay (all amounts due at separation) – generally within 30 calendar days from your last day, unless your CBA/company policy promises a shorter period.
Certificate of Employment (COE) – must be issued within 3 days of your request, even if clearance isn’t done.
BIR Form 2316 – must be given upon separation or by the annual deadline (you’re entitled to your copy).
13th-month pay – pro-rated up to your last day; usually included in final pay if you resign mid-year.
Service Incentive Leave (SIL) – unused 5 days/year (if you’re covered) are convertible to cash upon separation.

“Final pay” typically bundles: unpaid salary up to last day, pro-rated 13th month, cash conversion of unused SIL, approved but unpaid allowances/commissions, tax refund (if any), and separation pay if you qualify (e.g., authorized-cause retrenchment/closure—not typical for a voluntary resignation).

2) What employers may lawfully do during clearance

Require return of property: laptop, phone/SIM, tools, ID/access cards, vehicles, uniforms, documents, confidential materials.
Check financial accountabilities: unliquidated cash advances, corporate card charges, outstanding loans, toolkits, inventory shortages, damages supported by reports.
Offset verified amounts against your final pay**, but only if**:
- there’s clear basis and documentation (e.g., signed cash advance forms, inventory records, incident reports),
- you’re informed of the computation (itemized), and
- you’ve had a chance to contest disputed items.
Withhold a portion equal to documented accountabilities temporarily while computing—not hold everything for months on end without a paper trail.

They may NOT:

Refuse to issue a COE just because clearance isn’t finished.
Condition release of final pay on signing a quitclaim that waives valid claims (quitclaims are valid only if voluntary, for reasonable consideration, and without fraud/duress).
Make arbitrary deductions (e.g., “penalty” with no policy, forcing you to pay for normal wear-and-tear).
Lock down wages for “company convenience” or HR backlogs beyond a reasonable period.

3) Typical clearance scope (and how to prepare)

Property & access

Company assets (SNs, accessories), lockers, keys, security passes, e-mail/VPN deactivation, data return/certifications.

Finance

Cash advances, petty cash, corporate card, tool kits, sales inventory, fuel/transport cards, loan balances, post-dated reimbursements.

HR/Admin

Exit interview, handover memo, knowledge transfer checklist, project turnover receipts, IP/confidentiality undertakings (these survive employment).

What to do before your last day

List every asset you ever received; gather turnover receipts.
Liquidate all advances with receipts; submit expense reports.
Document the handover (owner, date, scope).
Request your COE in writing (email) before you leave; follow up 3 days later if needed.

4) Final pay: content, timing, and common disputes

A. What must be included

Salary to last day, overtime/night diff if any, pro-rated 13th month, unused SIL cash conversion, commissions/allowances that have become due and determinable, tax refund (if over-withheld), separation pay if the cause is employer-initiated (not ordinary resignation).

B. When it must be paid

Within ~30 days from separation (or earlier if your policy/CBA says so). HR “backlogs” are not a legal excuse for long delays.

C. What can be deducted

Documented losses or unreturned property (with incident/asset reports), signed loans/advances, lawful deductions (statutory, authorized in writing).
Not deductible: routine wear-and-tear, speculative losses, “training bonds” that don’t meet validity tests (must be reasonable, time-bound, clearly agreed, proportionate).

D. Interest & escalation

If final pay is unreasonably delayed after demand, employees commonly seek legal interest on money claims and damages in appropriate forums.

5) COE, tax, and records: your non-negotiables

COE (job title, dates, optionally pay if requested) – issue within 3 days of request, clearance status irrelevant.
BIR Form 2316 – needed for your next employer/ITR; insist on your copy.
Payslips & ledgers – ask for final itemized statement showing gross amounts, each deduction, and net.

6) Practical playbook when clearance is dragging

Step 1 — Write (politely) and set a clock

Email HR/Payroll and your manager: request (a) COE within 3 days, (b) final pay within 30 days of separation (or earlier per policy), (c) itemized clearance list with specific amounts/due dates.

Step 2 — Offer solutions

Propose a partial release (undisputed amounts now, balance after return/valuation of assets).
If a device is pending valuation, suggest market-based charge and immediate set-off so payroll can close.

Step 3 — Escalate internally

Copy the HR head/Finance, attach your asset return receipts and liquidation forms.

Step 4 — External remedies (fastest first)

SEnA (Single-Entry Approach) at DOLE: free conciliation-mediation, target 30 days to settle.
If unresolved, file a money claim (unpaid wages/benefits) at the NLRC. Bring your contract, company handbook, emails, turnover receipts, and pay records.
You may also complain to DOLE for COE non-issuance and unlawful deductions.

7) Special situations

A. Sales/commission roles

Post-separation commissions are payable if the sale was earned under your plan (e.g., booked/collected) and not validly clawed back by a written, reasonable policy.

B. Probationary employees

Same rights to final pay, COE, SIL cash-out (if covered) and 13th month pro-rated.

C. Gov’t-mandated contributions

Your last SSS/PhilHealth/Pag-IBIG remittances should be posted; you may request the R-3/ML-2 proof through HR.

D. Training bonds, scholarships, relocations

Valid training-cost recovery needs a written agreement, reasonable amount/timeframe, and a link to actual costs. “Liquidated damages” that look punitive are risky for employers. Disputed bonds shouldn’t justify indefinite payroll holds—ask for itemized computations.

E. Company housing, car plans, gadgets

If you keep the asset, expect valuation + set-off. If returned, delays should be limited to inspection time, not months.

8) Your documents & evidence checklist

Resignation letter and employer acknowledgment (with effective date).
Email requesting COE and final pay (keep timestamps).
Company policies/CBA pages on clearance and final pay timelines.
Asset turnover forms, gate passes, courier receipts.
Cash advance liquidation approvals, corporate card statements.
Latest payslips and commission plan.
Screenshots of HRIS tickets/approvals.
Any demand letter you sent and proof of receipt.

9) Sample short email you can copy-paste

Subject: Request for COE and Final Pay – [Your Name], Resigned Effective [Date]

Dear HR/Payroll, I resigned effective [Last Working Day, e.g., 15 Sept 2025]. Attached are my asset turnover receipts and liquidations.

Please issue my Certificate of Employment within 3 days of this request.

Kindly release my final pay (salary to last day, pro-rated 13th month, unused SIL conversion, tax refund/commissions if any), within 30 days from my last day or earlier if company policy provides. If any deductions apply, please send an itemized computation and supporting documents.

Thank you. [Name] | [Employee No.] | [Mobile] | [Personal Email]

10) FAQs

Q: Can the company hold all my final pay until every signature is done? A: They can verify accountabilities and withhold a reasonable, documented amount for specific items, but indefinite or blanket holds are improper. Ask for a partial release of undisputed sums.

Q: They refuse to give a COE until I’m “cleared.” A: A COE is yours on demand (within 3 days) regardless of clearance status.

Q: I won’t sign a quitclaim—can they withhold my pay? A: No. Pay that is due and demandable must be released. Quitclaims must be voluntary and for reasonable consideration to be valid.

Q: What if I lost a laptop? A: The employer may charge documented replacement/repair after due process (incident report, your explanation). Ask for valuation and receipts; negotiate depreciated value, not brand-new retail, unless policy says otherwise.

Q: How long do I have to file a claim? A: Money claims generally prescribe in 3 years from when they accrued. Don’t wait—documents get harder to collect later.

Bottom line

Clearance is process, not a license to delay what the law already requires.
Expect your final pay within about 30 days, your COE within 3 days of request, and itemized, documented deductions only.
If HR stalls, escalate politely in writing, then use SEnA (conciliation) and, if needed, NLRC to recover money claims—with potential legal interest for unreasonable delay.

If you tell me your last working day, what’s still “pending” in clearance, and what HR already said, I can draft a tailored demand email (or a concise SEnA request) and an itemized final-pay checklist for your case.