1) Why the question matters

In Philippine workplaces, “discipline” is usually tied to the employer’s management prerogative to regulate conduct and impose sanctions. Resignation, on the other hand, generally ends the employer–employee relationship. The practical collision happens when:

a notice to explain (NTE) has been issued but not resolved;
an investigation is ongoing when the employee resigns;
the employer discovers misconduct only after the resignation; or
the employer wants to “finish the case” to recover losses, deny certain benefits, or protect the company from future claims.

The key is to separate (a) disciplinary penalties that require an existing employment relationship from (b) fact-finding and post-employment remedies that do not.

2) Baseline concepts in the Philippine private sector

A. Resignation ends employment—usually

Resignation is a voluntary act of the employee to sever the employment relationship. Once effective, the employer typically loses the ability to implement employment-based penalties (e.g., suspension, demotion, dismissal) because there is no longer an employment status to suspend, demote, or terminate.

B. But misconduct doesn’t become irrelevant

Acts committed during employment may still have consequences after resignation, but those consequences shift from “employment penalties” to:

documentation and defense (e.g., to rebut later illegal dismissal claims);
clearance and accountabilities (return of property, liquidations);
lawful set-offs and claims (subject to strict limits);
civil claims (damages, recovery of company losses);
criminal complaints (e.g., qualified theft, estafa) where applicable; and
contract-based consequences (e.g., bond agreements, training reimbursement clauses—if valid and reasonable).

C. Due process remains relevant—even if dismissal is moot

In the private sector, “due process” in discipline typically refers to the two-notice rule and an opportunity to be heard before termination for just causes. When the employee resigns, the employer may no longer be pursuing termination, but procedural fairness still matters because the employer’s conclusions can affect:

the employer’s legal posture in future disputes;
the integrity of internal records;
eligibility for certain benefits under company policy (where lawful);
the defensibility of set-offs/claims; and
reputational and liability risks (defamation, data privacy, bad faith).

3) The short legal answer (private sector): “Proceeding” is possible, but “penalizing” is limited

A. Can the employer continue the disciplinary case after resignation?

Yes, the employer can continue the investigation and complete a finding on the incident (for internal governance and future legal defense), but the employer generally cannot impose employment-based penalties once the resignation is effective.

Think of it as two layers:

Investigative/administrative layer (fact-finding): can continue
Employment-penalty layer (suspension/dismissal/demotion): typically becomes unenforceable post-resignation

B. Can the employer still “terminate” someone who already resigned?

As a practical and legal matter, termination after effective resignation is largely moot because the relationship has already ended. Attempting to label it as “dismissal” after resignation can create confusion and risk—especially if it looks like retaliation or an effort to taint records without proper basis.

What employers usually can do instead is issue an internal case resolution (e.g., “finding of misconduct”) without purporting to “dismiss,” and then pursue lawful remedies (property recovery, civil/criminal action, etc.) if warranted.

4) The public sector is different: resignation generally does not stop administrative cases

If you are dealing with government employees (civil service), resignation does not automatically extinguish administrative liability. Administrative proceedings may continue despite separation from service, because the aim includes maintaining integrity of the public service and imposing administrative penalties that can survive separation (e.g., forfeiture of benefits in certain cases, disqualification from reemployment, etc., depending on applicable rules).

This article’s deeper “two-notice rule” discussion mainly fits the private sector; public sector cases are rule-driven under civil service frameworks where continuation after resignation is more straightforward.

5) Common scenarios and how Philippine practice typically treats them

Scenario 1: Employee resigns after receiving an NTE (pending explanation)

Employer may still require an explanation and set deadlines.
If the employee no longer participates, the employer can resolve the case based on available evidence.
The “resolution” is best framed as a finding (for records/legal defense) rather than an attempt to “dismiss” someone already out.

Risk to manage: If the employer later withholds pay or benefits based on a one-sided finding, it must be legally defensible; otherwise, it can expose the employer to money claims.

Scenario 2: Employee resigns during an ongoing investigation/hearing

Continue fact-finding; document non-attendance.
Offer a reasonable chance to respond (email + last known address).
Close the investigation with a written resolution.

Best practice: Make clear the purpose is to determine facts and liabilities relating to acts during employment, not to impose post-employment “punishment” that the employer has no power to enforce.

Scenario 3: Employer discovers misconduct only after resignation

The employer can investigate internally.
Employment penalties are no longer implementable, but the employer may:
- demand return of property;
- quantify losses and pursue recovery through lawful channels; and/or
- file civil/criminal complaints if justified.

Key point: Late discovery does not erase accountability, but it changes the remedy path.

Scenario 4: Resignation is used to evade discipline (“resign to avoid dismissal”)

In the private sector, this still doesn’t resurrect the employer’s power to impose employment penalties post-separation. But it strengthens the employer’s need to:

preserve evidence,
finalize an internal finding, and
pursue non-employment remedies (recovery of losses, legal action).

Employers also use the completed record defensively if the ex-employee later claims they were actually dismissed or coerced.

Scenario 5: Resignation is disputed (employee claims they were forced / constructive dismissal)

This is where the employer’s due process record becomes crucial.

If an employee later alleges:

resignation was involuntary,
they were threatened with baseless charges, or
the resignation was a product of coercion,

then an employer’s clean documentation helps show:

the employee had notice,
the employee had a fair chance to respond, and
the employer acted in good faith.

Conversely, a rushed “finding” without giving a real chance to be heard can backfire and support allegations of coercion or bad faith.

6) Due process standards in Philippine private-sector discipline (and how resignation changes the stakes)

A. Substantive due process: there must be a valid ground

Even if the employee has resigned, any internal finding should still be anchored on:

a recognized category of misconduct (often aligned with “just causes” concepts), and
a company rule/policy or a reasonable standard of behavior, supported by evidence.

An unsupported “guilty” label creates unnecessary risk.

B. Procedural due process: notice + opportunity to be heard

For termination, the classic template is:

First notice describing acts/omissions and giving time to explain
Opportunity to be heard (written explanation and/or conference)
Second notice stating the decision and reasons

After resignation, the employer’s goal is usually not termination but case closure. Still, procedural fairness matters because:

it demonstrates good faith;
it reduces the risk that the resolution is attacked as arbitrary; and
it helps justify follow-on actions (property recovery, legal claims).

Practical adjustment post-resignation: You can still do “two notices,” but the “decision notice” should avoid language implying a live employment penalty (e.g., “you are dismissed effective today”) if the resignation has already taken effect. Instead, use language like:

“case resolution / finding,”
“determination of accountability,” and
“directives for turnover/return/payment of accountabilities,” as applicable.

7) What the employer can do after resignation (private sector)

A. Continue fact-finding and issue a written case resolution

Permissible and often advisable:

complete the record while evidence is fresh,
state the findings and basis, and
document that the former employee was given the chance to respond.

B. Demand return of company property and confidential information

Even without an employment relationship, obligations to return property and protect trade secrets/confidential information can arise from:

ownership rights,
confidentiality agreements,
data privacy/security obligations, and
general law.

C. Pursue civil remedies to recover losses

If there is provable damage (e.g., fraud, misappropriation, breach of duty causing loss), the employer may:

demand payment formally, and
file a civil action if necessary.

D. Pursue criminal remedies where appropriate

If facts support a criminal offense, resignation does not bar the filing of a complaint. Criminal liability is personal and not dependent on continued employment.

E. Defend against future claims

A properly conducted investigation and resolution can be used to:

rebut allegations of forced resignation or illegal dismissal,
explain why certain actions were taken (e.g., withholding release of property clearance), and
demonstrate good faith.

8) What the employer generally cannot do after resignation (private sector), or can do only with caution

A. Impose employment-based penalties (suspension, demotion, dismissal)

Once the resignation is effective, these penalties generally lose practical and legal footing.

B. “Blacklist” in a way that becomes defamatory or unlawfully restrictive

Employers may keep internal records, but publishing accusations or sharing unverified derogatory information can create liability risks. Reference checks should be handled cautiously and truthfully, ideally limited to verified employment facts unless there is a clear lawful basis and careful phrasing.

C. Withhold final pay without legal basis

Employers commonly want to hold final pay pending “clearance.” In Philippine practice, withholding is a high-risk area. Employers should distinguish:

Legitimate accountabilities (unreturned property, documented cash advances, liquidated obligations) supported by clear records and lawful set-off rules; versus
Disputed damages/penalties that require adjudication or clear contractual authority.

A broad “we will not release anything until the investigation ends” stance can invite money claims and findings of bad faith if not grounded on lawful, documented offsets.

D. Force the employee to withdraw resignation or “not accept resignation” to keep discipline alive

An employer’s “acceptance” is not always the controlling factor if the resignation is valid and effective per notice and circumstances. Attempts to block resignation purely to impose discipline can be counterproductive and may inflame disputes.

9) Clearance, final pay, and the “accountability” overlay

A. Clearance is not a license to impose penalties

Clearance is primarily an administrative mechanism to ensure:

turnover,
return of assets,
settlement of advances, and
completion of documentation.

It should not be used as leverage to extract waivers or to impose punitive deductions.

B. Lawful deductions and offsets must be document-based and defensible

Deductions from pay generally require:

a clear basis (lawful/contractual/company policy consistent with law),
documentation (receipts, acknowledgments, liquidation reports), and
proportionality and reasonableness.

For alleged damages due to misconduct, if liability is contested, the safer path is often to:

document the claim,
pursue appropriate proceedings, and
avoid unilateral “penalty deductions” that look like self-help.

C. Release documents (COE, etc.)

Issuance of employment documents should be handled consistent with legal obligations and fair practice. If there is a legitimate dispute, it is better managed through clear communication and lawful process rather than blanket refusal.

10) Drafting the post-resignation disciplinary “resolution” the right way

If the employee has already resigned effectively, the employer’s final document should avoid framing that implies continued employment authority. Consider structuring it as:

Background
- employment period, role, relevant policies
Allegations / Incident Summary
Evidence Considered
- records, CCTV logs, emails, audit reports, witness statements
Opportunity to Respond
- dates and modes of service, any responses received, non-appearance noted
Findings
- facts established, policy provisions implicated
Conclusion
- determination of accountability (without stating “dismissal” if already resigned)
Directives
- return property, settle advances, data return/deletion certification (if applicable)
Reservation of Rights
- civil/criminal remedies, if warranted

This preserves due process posture while respecting the reality that employment penalties are no longer implementable.

11) Employee-side considerations: what a resigning employee should know

A. Resignation doesn’t erase liability for proven wrongdoing

Even if discipline cannot be “implemented” as employment penalties, legal liability (civil/criminal) can remain.

B. Participate (or respond in writing) to protect your record

If an employer continues an investigation post-resignation, providing a written response helps:

correct inaccuracies,
document defenses, and
reduce the chance of one-sided conclusions.

C. Watch for unlawful withholding or defamatory actions

If final pay is withheld without clear justification, or accusations are circulated recklessly, these can create separate legal issues.

D. If resignation was forced, document the coercion

If an employee claims constructive dismissal or forced resignation, contemporaneous evidence is critical (messages, witnesses, timelines).

12) Practical workplace checklist (private sector)

For employers

Preserve evidence immediately (audit trail, access logs, device imaging where lawful).
Serve notices to last known addresses/emails; give reasonable time to respond.
Hold a hearing/conference if feasible; document if the employee declines.
Issue a “case resolution” (not a “dismissal”) if resignation is already effective.
Separate accountabilities (property/advances) from damages claims (which may need adjudication).
Avoid blanket withholding of final pay; justify any offset with documentation and lawful basis.
Keep communications factual and need-to-know to reduce defamation/data privacy risk.

For employees

Provide a clear resignation notice and keep proof of service.
Respond to allegations in writing; request copies of evidence if appropriate.
Complete turnover and return property with documentation.
Keep records of any coercion or threats if resignation is disputed.

13) Bottom line

In the Philippine private sector, resignation generally ends the employer’s ability to implement disciplinary penalties that depend on an active employment relationship. However, the employer may still continue and complete an investigation into acts committed during employment, issue a written finding/resolution, require settlement of accountabilities, and pursue civil/criminal remedies where warranted—provided actions are evidence-based, procedurally fair, and do not rely on unlawful withholding or defamatory publication. In the public sector, administrative accountability can commonly proceed despite resignation under applicable civil service rules.