The shops – in Broomhouse and Sighthill – were targeted within a week of each other towards the end of January.
CCTV footage was obtained by the Evening News as police appealed for information on the raids, which saw the men leave with cigarettes and alcohol.
Now it has been confirmed that two men have been arrested in connection with the incidents, which left both shopkeepers terrified.
One of them, a 22-year-old male, is due to appear at Edinburgh Sheriff Court today, while another male has been remanded following an initial appearance.
A spokesman for Lothian and Borders Police said: “We are following positive lines of inquiry.”