How to Take the Deductions. The IRS allows you to deduct $5,000 in business startup costs and $5,000 in organizational costs, but only if your total startup costs are $50,000 or less.If your startup costs for either area exceed $50,000, the amount of your allowable deduction will be reduced by that dollar amount.ow to Take the Deductions. The IRS allows you to deduct $5,000 in business startup costs and $5,000 in organizational costs, but only if your total startup costs are $50,000 or less.