There are different Schengen visa categories. Most visitors from Non-EU countries like the US and Canada will receive a stamp in their passport upon entering the Schengen area. This is equivalent to getting a short-stay Schengen visa .
The short-stay visa is the most common Schengen visa. It entitles travellers, subject to the visa requirement, to enter the territories of the 25 Schengen States to pay a continuous visit or several visits, the duration of which does not exceed three months (90 days) in any half-year from the date of first entry in the Schengen area.After 90 days you will have to leave the Schengen area for a full 90 days to be legally allowed to re-enter. The short-stay visa is issued for one or several entries.
The single-entry visa allows one uninterrupted stay in the Schengen area whose duration does not exceed the number of days indicated on the visa, 90 days being the maximum of days which may be granted. A period of grace of 15 days of validity of the visa is normally added to the number of days of authorised stay, should the visa holder wish or have to postpone his or her departure.
The fact that immigrations officers do not check passports that much and usually let travelers leave without hassle after overstaying and even re-enter the Schengen area a few days later does not mean that the new stamp in the passport restarts the Schengen visa timeline for another 90 days. Basically you were lucky that no one noticed it or did not want to make a big fuss.This leniency changes dramatically when you apply for a work permit or a residence permit and you will find your work permit application denied as you do not have a valid visa which is required when you apply and also it still has to be valid when you go to collect the work permit.Also applying for a residence permit after overstaying does not go down well.
So the best advice is to apply for a temporary residence permit in Malta before your Schengen visa expires if you want to stay longer. Residence permits for Malta are issued in Malta and allow you to stay in Malta for more than 3 months. But you will need to give a reason !
Or apply for a long-term Schengen visa from your home country before you arrive.
You will be required to show that you can fulfill the other requirements such as health insurance and enough income to support you during your stay but
you will be legal!
Please feel free to comment and /or post personal experiences positive or negative for future reference.
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