Term Loans10 min readUpdated Feb 2026

Beyond the Interest Rate: The Hidden Fees in Business Loans (and How to Avoid Them)

Learn about origination fees, guarantee fees, prepayment penalties, and other costs that increase your loan expense. Understand why APR matters more than interest rate alone.

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When comparing business loans, most borrowers focus on interest rate. But interest is often just part of the cost. Fees can add thousands of dollars to your loan expense, sometimes making a "lower rate" option more expensive overall.

Understanding the full fee landscape helps you compare loan options accurately and negotiate better terms. Here's what you need to know about the hidden costs in business loans.

Why Fees Matter More Than You Think

Consider two loan offers for $100,000 over 5 years:

Loan ALoan B
Interest Rate7.0%8.0%
Origination Fee3.0%0%
Guarantee Fee0%0%
Packaging Fee$2,500$0
Upfront Cost$5,500$0
Total Interest$18,766$21,656
Total Cost$24,266$21,656

Loan A has a lower interest rate but costs $2,610 more overall due to fees. This is why comparing APR (Annual Percentage Rate), which includes most fees, beats comparing interest rates alone.

Common Business Loan Fees Explained

Origination Fees

Origination fees (also called processing fees or underwriting fees) cover the lender's cost to evaluate and fund your loan. They typically range from 0.5% to 3% of the loan amount.

  • Bank loans: Usually 0.5-1% for well-qualified borrowers. Sometimes waived for existing customers.
  • SBA loans: Lenders can charge up to 2% on portions over $50,000, plus other fees.
  • Online lenders: Often 1-5%, sometimes higher. May be called 'origination,' 'processing,' or 'administrative' fees.

Negotiation Point

Origination fees are often negotiable, especially at banks with which you have relationships. Ask directly: 'Can you reduce or waive the origination fee?' The worst they can say is no.

SBA Guarantee Fees

SBA loans include fees that fund the SBA's guarantee program. These are non-negotiable and based on loan amount and term:

Loan AmountGuarantee FeeAnnual Service Fee
Up to $150,0002% of guaranteed portion0.55% per year
$150,001 - $700,0003% of guaranteed portion0.55% per year
$700,001 - $1,000,0003.5% of guaranteed portion0.55% per year
Over $1,000,0003.5% of guaranteed portion0.55% per year

For a $500,000 SBA 7(a) loan with 75% guarantee, the upfront guarantee fee is approximately $11,250 (3% of $375,000), plus ongoing annual fees. These fees are typically rolled into the loan rather than paid upfront.

Prepayment Penalties

Prepayment penalties charge you for paying off your loan early. Lenders lose expected interest income when you prepay, so they recoup some of that through penalties.

  • SBA loans over $50,000: Penalty of 5% if prepaid in year 1, 3% in year 2, 1% in year 3. No penalty after year 3.
  • Bank loans: Varies widely. Some have no penalty, others charge declining percentages or interest minimums.
  • Online lenders: Some have no prepayment benefit at all - you owe the full factor rate amount regardless of when you pay.

Critical for Refinancing

If you think you might refinance when your credit improves or rates drop, prepayment penalties matter enormously. A 3% penalty on a $200,000 loan is $6,000 - which might wipe out any rate savings from refinancing.

Packaging and Broker Fees

If you use a loan broker or packager (common for SBA loans), they charge additional fees:

  • SBA packaging fees: Typically 1-3% of loan amount. Covers application preparation, documentation gathering, and lender matching.
  • Broker fees: Usually 1-2%, sometimes higher for complex deals. Compensates brokers for connecting you with lenders.
  • Referral fees: Sometimes built into the rate rather than charged separately. If your rate seems high, ask if there's a referral fee.

Line of Credit Fees

Lines of credit often have fee structures different from term loans:

  • Draw fees: 1-2% each time you draw funds. Adds up significantly with frequent draws.
  • Annual fees: $0-500+ per year regardless of usage. Covers account maintenance.
  • Inactivity fees: Some lines charge if you don't use them. Typically $25-100 monthly.
  • Minimum interest charges: Even if you repay quickly, you may owe minimum interest.

Other Fees to Watch

Various other fees can appear in loan agreements:

  • Application fees: $0-500 to apply. Non-refundable even if declined. More common with smaller lenders.
  • Documentation fees: $50-500 for preparing closing documents.
  • Wire transfer fees: $25-50 per transfer. Adds up with multiple disbursements.
  • Late payment fees: 5% of payment or $25-50 flat fee. Plus potential credit damage.
  • NSF/returned payment fees: $25-50 if your payment bounces.
  • Account maintenance fees: Monthly or annual fees on some loan accounts.
  • UCC filing fees: $50-200 for filing security interest documents.
  • Legal fees: For larger loans, you may pay the lender's legal costs.

Why APR Is Better Than Interest Rate

Annual Percentage Rate (APR) incorporates most fees into a single comparable number. It represents the true annual cost of borrowing including interest and fees. The Truth in Lending Act (TILA), enforced by the Consumer Financial Protection Bureau (CFPB), requires lenders to disclose APR to help consumers compare loan costs.

MetricWhat It IncludesUse For
Interest RateInterest charges onlyUnderstanding base cost
APRInterest plus most feesComparing total loan costs
Total Cost of CapitalEverything including opportunity costComplete analysis

Under the Truth in Lending Act, lenders must disclose APR, though calculation methods vary slightly. Note that APR disclosure requirements differ for consumer and business loans - business loans may have less standardized disclosures. When comparing loans, always compare APR, not just interest rate.

APR Limitations

APR doesn't include all costs. Prepayment penalties, late fees, and some closing costs may not be reflected. For the fullest picture, list all fees and calculate total repayment amount.

How to Identify Hidden Fees

Protecting yourself requires diligence during the loan process:

  • Request a full fee schedule: Ask explicitly for a list of all fees before applying. Reputable lenders provide this readily.
  • Review the loan estimate carefully: This document should itemize all costs. Question anything unclear.
  • Ask about fees not listed: 'Are there any fees not shown here that I might incur?'
  • Compare total cost, not just rate: Calculate total dollars repaid under each option.
  • Read the fine print on prepayment: Understand exactly what happens if you pay early.
  • Understand the payment structure: Daily payments can make effective rates higher than quoted.

Negotiating Fees

Many fees are negotiable if you know to ask. Here's what's typically flexible:

Fee TypeNegotiabilityStrategy
Origination FeeOften negotiableAsk for reduction or waiver, especially with banking relationship
Application FeeSometimes waivedAsk before applying; leverage competing offers
Documentation FeeModestly negotiablePush back; these are often profit centers
Prepayment PenaltySometimes negotiableRequest removal or reduction before signing
SBA Guarantee FeesNot negotiableSet by SBA; same with all lenders
Wire Transfer FeeSometimes waivedRequest ACH instead of wire
Late FeesNot usuallyFocus on never paying them

Use Competition

Get 2-3 loan offers and use them as leverage. 'Lender B is offering the same rate with lower fees. Can you match that?' Even if you prefer Lender A, competition drives better terms.

Red Flags in Fee Structures

Certain fee practices suggest predatory lending or poor value:

  • Fees exceeding 5% of loan amount: Unless you have very poor credit, total fees shouldn't approach this level.
  • Mandatory insurance: Some lenders require you to buy insurance products that benefit them.
  • Vague fee descriptions: "Processing fee," "admin fee" without specifics may hide excessive charges.
  • Fees charged on declined applications: Legitimate lenders don't charge much if they don't fund you.
  • No prepayment benefit: Owing the same amount whether you repay in 3 months or 12 months is a red flag.
  • Rapidly changing fee quotes: If fees keep changing during the process, the lender may be untrustworthy.

The Bottom Line

Interest rate is important, but it's only part of your loan cost. Origination fees, guarantee fees, prepayment penalties, and various other charges can add thousands to your total expense and even flip which loan is cheapest.

Always compare APR rather than interest rate. Request complete fee schedules before applying. Calculate total dollars out of pocket under each scenario. Negotiate fees where possible - many lenders have flexibility, especially for well-qualified borrowers or those with competing offers.

The few hours spent understanding and comparing fees can easily save you thousands of dollars. That's time well invested in your business's financial health.

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Important Disclosure

Not Financial Advice: The information provided in this article is for general informational purposes only and does not constitute financial, legal, or professional advice. You should consult with qualified professionals before making any financial decisions.

No Guarantee of Financing: Liminal Lending Co. is a business loan marketplace that connects borrowers with third-party lenders. We are not a lender and do not make credit decisions. Submitting an application does not guarantee approval or funding. Loan terms, rates, and availability vary by lender and are subject to borrower qualifications and lender criteria.

Third-Party Lenders: All loan products are offered by independent third-party lenders. Liminal Lending Co. is an Independent Sales Organization (ISO) and receives compensation from lenders for successful referrals. Terms and conditions of any loan are between you and the lender.

Rate Information: Rates, terms, and fees mentioned in this article are estimates based on publicly available information and may not reflect current market conditions or specific lender offers. Actual rates depend on creditworthiness, business financials, and lender policies.

Information May Change: Financial markets, lending regulations, and economic conditions are subject to rapid change. While we strive to keep our content accurate and up-to-date, information in this article may become outdated. Always verify current rates, terms, program availability, and regulatory requirements with lenders and official sources before making financial decisions.