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A large group of independent pharmacy owners usually end up owning some form of real estate. Sometimes it is the building the pharmacy operates out of. Sometimes it is a short term rental or a second property picked up along the way. Often all of it ends up in the same place, on Schedule E of the personal tax return. For some owners, that is the right spot. For many, it is not. The problem is not that Schedule E is always wrong. The problem is that the decision usually was no

We continue to see this pattern month after month with independent pharmacy owners. They have every element in place for a lower tax bill. The pharmacy entity. Sometimes a separate entity that owns the building the pharmacy operates out of, which pays rent to that entity. Sometimes a rental property on the side. Sometimes a spouse running a completely separate business. Each piece, on its own, is fine. Filed correctly, nothing flagged, nothing broken. The problem is nobody is

Independent pharmacy owners normally set up their business structure once, when they bought or opened the pharmacy, and never look at it again. That's a mistake. The tax code changes. Your revenue changes. What made sense five years ago may be costing you thousands today. If you're not sure whether you're a sole proprietor, an LLC, or an S corp, or you set it up years ago and haven't thought about it since, this is worth ten minutes of your time. How pass-through taxation act

If you own an S-corp and you work in the business, the IRS requires you to pay yourself a W2 wage. Most pharmacy owners know that much. What trips people up is the amount. There is no formula for this. No 60/40 split. No calculator that spits out a compliant number. The IRS evaluates reasonable compensation based on facts and circumstances: what you would pay someone else to do your job, what comparable businesses pay for similar roles, and what your specific market demands f

We support APC’s mission and long-standing advocacy on behalf of independently owned pharmacies and the patients they serve. This relationship reflects a shared commitment to strengthening the future of pharmacy, including compounding within independent practice. As part of this relationship, APC Pharmacy/Facility Members will receive a preferred services benefit with Medari Advisors. Contact a Medari Advisors for details and discount information. Medari Advisors provides tax

Every year, pharmacy and clinic owners spend thousands of dollars on scrubs, staff meals, client lunches, and gifts. Some of it gets deducted. Most of it does not. And with the One Big Beautiful Bill Act signed into law in 2025, the rules changed again starting January 1, 2026. Here is what you can actually write off, what just changed, and what you need to document to make it stick. Scrubs and Uniforms: The Deduction Most Healthcare Owners Miss If your staff wears scrubs, th

Most independent pharmacy owners and healthcare clinic owners know how much they paid in taxes last year. Far fewer know whether they paid more than necessary. That is a problem. A tax return tells you what happened. It does not always tell you whether better planning could have reduced your tax exposure, improved your cash flow, or helped you make smarter business decisions before the year ended. Many business owners only hear from their accountant during tax season. They se

When many independent pharmacy owners start their business, the entity structure decision feels simple. Set up an LLC. Open the bank account. Start filling prescriptions. Keep moving. At the beginning, that may be perfectly fine. For many owners, it is the right place to start. The problem begins when the business grows, profit increases, payroll changes, new services are added, real estate enters the picture, or the owner starts taking more money out of the business. What wo

Most people assume taxable income only comes from a paycheck or business revenue. The IRS disagrees. There are a number of situations where money, benefits, or items received may create taxable income, even when people do not expect it. Business owners are often surprised to learn how broad the IRS definition of income really is. Here are some of the most common areas of confusion. Unemployment Compensation Unemployment compensation is generally considered taxable income at t

Most pharmacy owners don't switch accountants because something is clearly broken. They stay because nothing feels urgent. Returns get filed. Numbers look fine. Taxes get paid. But that doesn't mean your CPA is performing well. And the margin for error here has gotten thinner: independent pharmacy gross margin fell to 18.2 percent in 2024, the lowest point the NCPA Digest has tracked. A CPA who is only filing clean returns isn't giving you enough room to work with anymore. If

Section 179 and bonus depreciation are not the same thing, and using the wrong one at the wrong time costs pharmacy owners real money. Section 179 lets you choose exactly which equipment purchases to deduct immediately and which to spread out. Bonus depreciation is all or nothing across an entire asset class. For 2026, bonus depreciation sits at 100 percent, and the Section 179 limit is $2,560,000. What Each One Actually Does Bonus depreciation is automatic and broad. Once yo

Cash flow issues in independent pharmacies rarely come from obvious problems. In most cases, the pressure builds from processes that appear stable but create timing gaps between when revenue is earned and when cash is received. That gap has gotten harder to absorb: independent pharmacy gross margin fell to 18.2 percent in 2024, the lowest point the NCPA Digest has tracked. If you only look at revenue and profit, you miss where cash is getting tied up. These are four areas tha

The tax code is about 75,000 pages long, so it's not surprising there are many overlooked money-saving deductions hidden within it. Check out this list of commonly overlooked deductions. You might wind up with a bigger refund than you expected. State sales tax alternative You can choose to deduct state and local sales taxes rather than state income taxes on a return using itemized deductions. This is especially useful for residents of states that don't have state income taxes

Most pharmacy owners and healthcare professionals focus on deductions when thinking about taxes. Deductions help, but they only address one side of the equation. Another strategy involves income the IRS never taxes. The tax code allows certain types of income to be received tax free when structured properly. These opportunities often appear in retirement planning, employer benefits, investment choices, and major financial decisions. Business owners frequently overlook these a

Mixing personal and business money costs you three ways: it multiplies the time and cost of accounting cleanup, it causes accountants to skip legitimate deductions out of caution, and it weakens the liability protection an LLC or S corporation is supposed to provide in the first place. Most business owners did not start their company because they love bookkeeping. They started because they are good at their craft. Over time a common habit shows up. Personal expenses start run

Pharmacy and healthcare business owners spend most of their time focused on patients, prescriptions, staff, inventory, and the daily operational demands of running a healthcare business. Financial statements often become something that gets reviewed quickly or saved for tax time. That approach leaves valuable information unused. Clean, accurate financial statements are one of the most useful tools a business owner has. They provide a clear view of how the business is performi

Owning a home comes with more than a mortgage payment. There are several tax benefits built into homeownership, but many taxpayers either miss them or misunderstand the limits. Here is a practical summary of the most common ones. Mortgage interest deduction Mortgage interest is one of the few types of personal interest that remains deductible. The deduction applies to up to $750,000 of mortgage debt on your primary residence. If your mortgage originated before 2018, the limit

Choosing the right accounting firm for a pharmacy is less about finding someone who files returns and more about finding someone who understands how your business actually works.

Fixing even one of these improves cash flow, reduces stress, and gives owners back control.

The IRS has announced the standard mileage rates for 2026. These rates are used to calculate the deductible cost of operating a vehicle for specific purposes. 2026 Standard Mileage Rates Business travel: 72.5 cents per mile (up 2.5 cents) Medical and moving: 20.5 cents per mile (down 0.5 cents) Charitable work: 14 cents per mile (unchanged) These rates apply to gas, electric, hybrid-electric, and diesel vehicles . What the IRS Means by Each Category 1) Business Travel Busi