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Botwinick

Navigating the Tax Implications of a Merger or Acquisition

Ken Botwinick, CPA | 11/24/2025

Whether you’re selling your business or acquiring another company, the tax structure behind the transaction can significantly influence its success. Understanding how taxes apply to mergers and acquisitions is essential to preserving value, minimizing risk, and ensuring long-term profitability.

Choosing the Right Structure: Asset Sale vs. Stock Sale

From a tax perspective, a merger or acquisition is generally structured as either an asset sale or a stock sale — and the choice makes a major difference in how much tax is paid.

Asset Sale

In an asset sale, the buyer acquires only selected assets of the business. This structure is commonly used when the buyer wants specific divisions, product lines, or intellectual property. It’s also the default method when purchasing a sole proprietorship or a single-member LLC treated as a sole proprietorship for tax purposes.

Stock Sale

If the business is a corporation, partnership, or an LLC taxed as a partnership, a buyer may acquire the seller’s stock or ownership interest directly. The tax outcome depends heavily on whether the business is a C corporation or a pass-through entity such as an S corporation, partnership, or LLC.

How Entity Type Affects Tax Liability

C Corporations

The current flat federal corporate tax rate of 21% makes stock purchases of C corporations more appealing to buyers. Lower corporate taxes mean potentially stronger after-tax earnings and reduced tax on future asset appreciation when sold.

Pass-Through Entities

Businesses structured as S corporations, partnerships, or LLCs generally pass income through to the owner’s individual tax return. Lower individual tax rates and the potential eligibility for the qualified business income (QBI) deduction may provide strong tax advantages to buyers considering these entity types.

In certain transactions, a stock purchase may be treated as an asset purchase using a Section 338 election. Speak with Botwinick & Co. to determine whether this strategy may work for your deal.

Which Party Benefits More? Seller vs. Buyer

Why Sellers Prefer Stock Sales

  • Typically results in lower overall tax liability.
  • Transfers most liabilities to the buyer.
  • May qualify for long-term capital gain treatment.

Why Buyers Prefer Asset Purchases

  • Helps reduce exposure to unknown or undisclosed liabilities.
  • Allows for a step-up in basis on acquired assets.
  • Enables increased depreciation and amortization deductions.
  • May reduce taxable gain when assets are later converted to cash or sold.

Buyers often prioritize cash flow after closing — especially if acquisition financing is involved. A structure that optimizes deductions and minimizes liability is typically best suited to meeting those financial objectives.

Other Factors to Consider

While tax planning is essential, several additional elements can influence the structure of a merger or acquisition, including:

  • Employee benefits and compensation plans
  • Retirement plans and deferred compensation
  • State and local tax obligations
  • Intellectual property valuation
  • Industry-specific compliance requirements

Plan Ahead with Tax Strategy — Not After the Deal Closes

Selling the company you’ve worked hard to build — or stepping into business ownership through acquisition — may be the most important financial decision you’ll ever make. With proper tax planning, you can avoid costly surprises and structure your transaction for maximum benefit.

Botwinick & Co. specializes in tax-smart merger and acquisition strategies for businesses of all sizes. We’ll help you evaluate the tax consequences before negotiations begin to ensure your interests are protected.

Ready to Discuss Your Transaction?

Let our experienced tax advisors guide you through the process. Contact Botwinick & Co. today to get started.

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Ken Botwinick, CPA Partner, CPA
Ken Botwinick, CPA is a Partner with Botwinick & Company, LLC and has been with the firm for more than 25 years. Ken specializes in providing accounting, tax, and business consulting services to dental and medical practices. He established the firm’s dental practice and is a sought-after lecturer at dental continuing education programs. Ken has his “finger on the pulse of the dental industry,” and with comprehensive experience in ownership transitions, he assists clients in the healthcare industry to reach their professional and financial aspirations and goals.
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About Ken Botwinick, CPA

Ken Botwinick, CPA is a Partner with Botwinick & Company, LLC and has been with the firm for more than 25 years. Ken specializes in providing accounting, tax, and business consulting services to dental and medical practices. He established the firm’s dental practice and is a sought-after lecturer at dental continuing education programs. Ken has his “finger on the pulse of the dental industry,” and with comprehensive experience in ownership transitions, he assists clients in the healthcare industry to reach their professional and financial aspirations and goals.

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