Officers carried out searches at properties in Loganlea Terrace, Lochend Road and Thorntree Street on Thursday evening. Crack cocaine with an estimated value of £25,500 was seized with £20,000 worth of cocaine and herbal cannabis with a value of around £24,000.
A quantity of heroin and a five-figure sum of cash were also recovered.
The men, aged 37 and 39, are scheduled to appear at Edinburgh Sheriff Court on Monday.
DI Stuart Harkness said: “Thanks to vital intelligence from the public, we have seized a sizeable quantity of dangerous drugs.”