Skip to Content

Small Business Tax & Small Accounting Challenges

What Startups, E-Commerce, Real Estate & Manufacturing Owners Must Know
January 9, 2026 by
Small Business Tax & Small Accounting Challenges
MTB CPA

Running a small business involves far more than making sales. From startup tax compliance to e-commerce accounting, real estate structuring, and manufacturing cost control, business owners face tax and accounting challenges that can quietly grow into costly problems.

As a small business CPA firm, we work closely with startups, e-commerce sellers, real estate investors, and manufacturing businesses. Across industries, we consistently see the same challenges arise—usually not because of mistakes, but because the right questions were never asked early enough.

Book a Free Small Business Accounting Review

 No obligation. CPA-led review for startups, e-commerce, real estate, and manufacturing businesses.

 1. Choosing the Right Business Structure for Small Business Tax Efficiency

One of the most critical small business tax decisions is choosing the correct entity structure before forming the organization.

This is especially important for:

  • Real estate businesses holding multiple properties

  • Startups planning to scale or raise capital

  • Manufacturing companies with operational and liability risk

  • E-commerce businesses selling across multiple states

In practice, businesses often require:

  • Separate entities to protect real estate assets

  • Different structures for operations versus asset ownership

  • A mix of S-Corporations, partnerships, and single-member LLCs—each aligned with a specific purpose

Take our Quiz to see the best structure for your business

 2. Selecting Accounting Software That Supports Compliance & Growth

Choosing accounting software is not just a technical decision—it’s a tax and compliance decision.

This challenge is common among:

  • E-commerce CPA clients using Shopify or Amazon

  • Manufacturing businesses tracking inventory and cost of goods sold

  • Startups preparing financials for investors or lenders

Key questions every business should consider:

  • How will sales data flow from Shopify or Amazon into accounting?

  • Will the software support sales tax tracking and reporting?

  • Can it handle inventory, payroll, and reporting together?

  • Will it produce clean, tax-ready financial statements?

 3. Managing Startup Tax Compliance Year-Round

Startup tax compliance is often misunderstood as an annual task. In reality, compliance happens on a monthly, quarterly, and annual basis.

Small businesses must manage:

  • Federal income taxes

  • State income taxes

  • Payroll taxes (Form 941, W-2s, state workforce reporting)

  • Sales tax filings (monthly or quarterly, depending on volume)

Common questions business owners face:

  • Am I required to file sales tax monthly or quarterly?

  • How do I properly document meals and travel expenses?

  • What receipts must be retained—and for how long?

  • Which payroll systems ensure compliance with state agencies?

Texas Tax Due Dates for Small Business Tax Compliance

Book a Free Small Business Accounting Review

 No obligation. CPA-led review for startups, e-commerce, real estate, and manufacturing businesses.

 4. Understanding Financial Reports That Reflect Real Performance

Many business owners receive reports—but don’t know which ones actually matter.

This is especially common for:

  • E-commerce businesses reviewing Amazon and Shopify reports

  • Manufacturing companies tracking product, overhead, and admin costs

  • Startups evaluating profitability and cash flow

Key questions include:

  • Are profits real—or just accounting profits?

  • Are product and inventory costs calculated accurately?

  • Are advertising, fulfillment, and administrative costs allocated properly?

  • Do reports reflect true operational performance?

 5. Sales Tax Compliance for Online & Multi-State Businesses

Sales tax is one of the most complex areas of small business tax, particularly for online sellers.

This affects:

  • E-commerce businesses selling into multiple states

  • Manufacturing companies shipping products across state lines

  • Startups scaling rapidly

Business owners must understand:

  • Where sales tax nexus exists

  • Who is responsible for collecting and remitting sales tax

  • Which reports to rely on from Shopify or Amazon

  • How often filings are required

Sales tax mistakes often surface later—with penalties and interest.

 6. How to Choose the Right Small Business CPA

Choosing the right CPA is not about finding the cheapest option—it’s about finding the right fit for your business.

A strong small business CPA should understand:

  • Startup tax planning and compliance

  • E-commerce accounting systems

  • Real estate tax structuring

  • Manufacturing cost and inventory accounting

  • Day-to-day business operations, not just tax forms

At MT Bachani CPA, our team has hands-on experience supporting small businesses across industries. We understand the pressures of running a business and design accounting and tax systems that work in real life—not just on paper.

Schedule a Small Business Tax & Accounting Review

No obligation. CPA-led review for startups, e-commerce, real estate, and manufacturing businesses.

E-Commerce CPA  | MT Bachani CPA | CPA Services for Amazon, Shopify, TikTok & 3PL-Driven Brands
We Understand E-Commerce Accounting — Cash vs Accrual the Right Way