If using the {{%-syntax it will work as expected as long as you don’t have surrounding html-elements in your shortcode (black friday will not parse markdown inside of html-elements). But because it is usual to have html in the shortcode you have to work around it, see Shortcode - markdown vs html vs table of content for a possible solution.
Also: 0.55 - What am I doing wrong?
You could also use the {{<-syntax and then do {{ .Inner | markdownify }} in your shortcode, as described by @Grob above.