In San Jose Wellness v. Commissioner 156 TC 4 (2021), the Court ruled that depreciation and charitable deductions made by the business were not deductible.
Section 280E reads:
“No deduction or credit shall be allowed for any amount paid or incurred during the taxable year in carrying on any trade or business if such trade or business (or the activities which comprise such trade or business) consists of trafficking in controlled substances (within the meaning of schedule I and II of the Controlled Substances Act) which is prohibited by Federal law or the law of any State in which such trade or business is conducted.”

The Tax Court opined that since marijuana is a controlled substance, that 280E applied to the pot store. Thus essentially, Pot stores are taxed on their gross income.
Remarkably though Pot stores can deduct costs of goods sold however. CHAMP v. Commissioner 128 TC 173 (2007).