The six stages: from application to final payment
EU funding in Malta under the investment schemes (SME Enhance and Digitalise your SME) follows a structured sequence. Understanding where you are in that sequence, and what each stage requires, affects both the timeline and the total grant received.
Application submission at a cut-off
The process starts with submission of a complete application through sfd.gov.mt before a cut-off date. Applications run on a biweekly schedule. All applications submitted before a given cut-off are assessed in the same batch. A late submission misses that batch and carries forward to the next cut-off. The cut-off schedule and current dates are published on fondi.eu.
Assessment by MSD
Following the cut-off, the Measures and Support Division (MSD) assesses the batch. Assessment covers applicant eligibility, project eligibility, financial standing, procurement compliance, and State Aid position. MSD may raise clarification requests during this stage. A formal approval or rejection decision is issued in writing. There are no published assessment timelines in the Guidance Notes; check fondi.eu for any updates on processing periods for the current call.
Grant Agreement signed
An approved application results in a Grant Agreement setting out the eligible costs, the approved grant amount, the implementation period, the advance payment schedule, and the conditions of award. The Grant Agreement date is the starting point for all subsequent milestones. Costs incurred before this date are absolutely ineligible. The implementation period clock starts from signature, not from the cut-off date or the approval date.
First advance payment
The first advance is triggered by the Grant Agreement signature. For Investment Aid and De Minimis applications, it equals 50% of the 7% indirect cost flat rate element of the approved grant. For start-up track applications, it equals 100% of the indirect cost flat rate element plus up to one year of eligible premises lease costs. This advance helps fund the early stages of implementation before the main costs are incurred.
Second advance payment (mid-implementation)
A second advance is available at a mid-implementation milestone. For Investment Aid and De Minimis applications, it equals 30% of the eligible grant attributed to the main investment component or components. For start-up track applications, it is capped at the eligible grant amount for the relevant component. Total advance payments across both stages cannot exceed 40% of the total approved eligible grant.
Final claim and reimbursement
Once implementation is complete, the beneficiary submits a reimbursement claim to MSD with all required documentation. The claim must be submitted within three calendar months of the Grant Agreement end date. MSD verifies the claim against the documentary evidence. The grant balance — total approved grant minus advances already paid — is released after successful verification.
Implementation period structure
The implementation period is set in the Grant Agreement and runs from the signature date. Under the investment schemes, the period is fixed at one of four durations: 6 months, 12 months, 18 months, or 24 months. The choice is agreed at the application stage and reflects the realistic scope and timeline of the investment.
For the advisory schemes, implementation periods are shorter and scheme-specific:
- Business Reports for SMEs: as agreed in the Grant Agreement; final programme deadline is 30 June 2029
- Internationalisation Strategy for SMEs: up to 12 months (fixed at 6 or 12-month periods)
- Marketing Strategy for Micro and Small Enterprises: fixed 6 months from the Grant Agreement
- Standards and Awards for SMEs: up to 18 months (fixed at 6, 12, or 18-month periods)
The implementation period is the window in which eligible costs must be incurred. Costs incurred after the end date are not eligible. All purchased assets should be in place, invoiced, and paid before the end date to be included in the reimbursement claim.
Advance payments: what to expect when
The advance payment structure under the investment schemes provides partial funding ahead of the final reimbursement claim. The two stages are as follows.
First advance: on Grant Agreement signature
| Track | First advance amount |
|---|---|
| Investment Aid (GBER) | 50% of the 7% indirect cost flat rate element of the approved grant |
| De Minimis | 50% of the 7% indirect cost flat rate element of the approved grant |
| Start-up track | 100% of the indirect cost flat rate element, plus up to 1 year of eligible premises lease costs |
Second advance: mid-implementation milestone
| Track | Second advance amount |
|---|---|
| Investment Aid (GBER) | 30% of eligible grant for the main investment component(s) |
| De Minimis | 30% of eligible grant for the main investment component(s) |
| Start-up track | Capped at the eligible grant amount for the relevant component |
Across both stages, total advance payments cannot exceed 40% of the total approved eligible grant. The balance — at least 60% of the grant — is paid only after MSD has verified the final reimbursement claim. This means the majority of the grant comes at the end, after you have funded the full investment from your own resources or financing.
Advance payments are not available under the advisory schemes. Those schemes reimburse costs after the advisory service has been delivered and verified.
Claim submission window
The reimbursement claim must be submitted to MSD within three calendar months of the Grant Agreement end date. This window is fixed; it does not flex based on when the investment was completed. If the investment is completed a month before the end date, the claim window still runs from the end date, not from the completion date.
The documentation required at the claim stage:
- All invoices for eligible expenditure, matching the approved cost schedule
- Proof of payment for each invoice
- Bank statements for the relevant period, certified by a Certified Public Accountant (CPA)
- Delivery records and photographic evidence of assets acquired
- An asset inventory
- Compliance certificates from the Malta Tax and Customs Administration (MTCA) covering income tax, VAT, Fringe Benefit Tax (FSS), and social security contributions
- A final implementation report
- Any additional documents specified in the scheme's Practical Guidelines
Outstanding payments — where an invoice has been received but not yet settled — are not eligible for reimbursement at the claim stage. All costs must be paid in full before submission.
Late claims and extensions
Late claim penalties
A reimbursement claim submitted after the three-month window closes incurs a 0.5% monthly deduction on the amount due. The deduction accrues from the day after the window closes and continues for each full month of delay. A claim submitted two months late on an approved grant of €80,000 would be reduced by 1%, or €800, before payment is made.
Extension requests
If the investment cannot be completed within the original implementation period, an extension can be requested. Extensions are available in 6-month blocks, subject to MSD approval. The request must be submitted before the current end date passes; a request submitted after the end date has passed incurs additional penalties.
| Extension scenario | Penalty |
|---|---|
| First 6-month extension block (requested before end date) | No deduction |
| Each subsequent 6-month extension block | 1% deduction per block |
| Extensions taking total implementation beyond 36 months | 2% deduction per 6-month block |
| Extension request submitted after the original end date has passed | Additional 5% penalty on top of any block penalties |
The penalty structure is designed to incentivise timely implementation. A business that requests a single 6-month extension in advance incurs no penalty. One that misses the end date without having requested an extension first, and then tries to submit retroactively, faces a 5% penalty on top of whatever subsequent extension penalties apply. Extensions are not automatic — MSD must approve them, and approval is not guaranteed.
For the full application process, including what MSD checks and the financial standing requirements, see the article on how EU funding applications are assessed in Malta. For common reasons applications and claims are rejected, see 5 reasons EU funding applications get rejected in Malta. For a full overview of all six active EU schemes in Malta, or to discuss a specific project, see our EU Funding Advisory service or contact us directly.
Frequently asked questions
How long is the implementation period for EU funding in Malta?
Under the investment schemes, the implementation period is up to 24 months from the Grant Agreement date, agreed at approval stage at 6, 12, 18, or 24 months. For the advisory schemes: Marketing Strategy runs for a fixed 6 months; Internationalisation Strategy for up to 12 months; Standards and Awards for up to 18 months. All schemes have a final programme deadline of 30 June 2029.
Can I receive a cash advance before the project is complete?
Yes, under the investment schemes. The first advance is paid on signing the Grant Agreement; the second at a mid-implementation milestone. Together they cannot exceed 40% of the total approved eligible grant. The remaining balance is settled after final claim verification. Advance payments are not available under the advisory schemes.
What happens if I miss the 3-month claim window?
A late claim incurs a 0.5% monthly deduction on the amount due from the day after the window closes. If no claim is submitted at all, the grant entitlement is forfeited with no mechanism for reinstatement.
Can I extend my EU grant implementation period in Malta?
Yes, in 6-month blocks with MSD approval. The first extension block carries no penalty if requested before the current end date. Subsequent blocks cost 1% per block; extensions beyond 36 months cost 2% per block. A request submitted after the end date has already passed carries an additional 5% penalty.
When does the first advance payment come through?
On signing the Grant Agreement. For Investment Aid and De Minimis applications, the first advance equals 50% of the 7% indirect cost flat rate element of the approved grant. For start-up applications, it equals 100% of the indirect cost flat rate plus up to one year of eligible premises lease costs.