The ban on smoking does apply to cafes and bars which are staffed by their owners, Arnhem appeal court ruled on Thursday.
Earlier, cafes in Breda and Groningen were found not guilty of breaking the smoking ban because the operations had no staff.
The ban was brought in to protect workers from second hand smoke and so did not apply to owner-operated bars, the lower courts had ruled.
In February, the high court ruled the ban could be applied to one-man operations without staff and ordered the Breda and Groningen cases to be heard again.
Some 40% of bars and cafes are thought to still allow smoking.
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