Mickelson's seven-under-par 65 included six birdies on the closing nine as the four-times Major winner closed to within three shots of Molinari (67) whose 54-hole 17-under total of 199 put him a stroke ahead of Dane Anders Hansen (65).
World number one Donald, tied for ninth with six others, mixed seven birdies with three bogies en-route to a 68, a shot behind Mickelson, home favourites Martin Laird (64) and Peter Whiteford (66) and Swede Alexander Noren (70).
Another Scot Marc Warren (64) was 15 under alongside Denmark's Soren Kjeldsen (64) as the field made the most of the benign conditions at the Castle Stuart course.
"My golf and my form are getting better and better," said Italian world number 28 Molinari.
"Obviously, it's a very good time to be playing this well, and I'll just see how it goes tomorrow. However it goes, I know I'm going to be at Lytham playing well," Molinari said of next week's British Open at Royal Lytham & St Annes in England.