UPDATED April 20, 2016: Code section 280E supposedly requires disallowance of all expenses other than cost of goods sold, but “[c]urrently, some IRS agents are accepting 280E allocations that disallow 20% to 25% of the expenses (other than Cost of Goods Sold).” That only 25% quote comes from a publicly posted draft publication of the BOTEC Analysis Corporation, http://www.liq.wa.gov/publications/Marijuana/I-502/small_business_impact_statement/botec_white_paper_1.pdf.
Here’s an elaboration: “Based upon the current situation with IRS auditors, it might be reasonable to assume that Section 280E will reduce expenses available for deduction by 20%; so as a baseline we have entered the Section 280E Disallowance Rate at 20%. (This is an assumption wrought with issues that are beyond the scope of this paper.)”