SMB Accounting · Payments guide
Taking Payments with QuickBooks: QuickBooks Payments vs Connecting Square, Stripe or PayPal
If you run your books in QuickBooks, you can take payments on your invoices and in person with QuickBooks' own payment service, or connect another processor such as Square, Stripe or PayPal. Here's how each one connects to QuickBooks, what you pay when a customer pays, and how long the money takes to reach your bank.
By Riley Park · Last verified: October 2026
The short answer
For most QuickBooks users, QuickBooks Payments is the simplest choice: it's built in, charges a flat 2.99% when a customer pays an invoice by card (2.5% in person), deposits the next business day, and records every payment in your books automatically.
Connecting another processor makes sense in a few cases: you already run a shop counter on Square, you sell online through Stripe, your customers prefer PayPal, or your clients often pay large invoices from their bank account, where QuickBooks' 1% bank-transfer fee has no upper limit. The sections below compare each option on what you pay, how it connects to QuickBooks and how fast you're paid, and the bottom line matches each to the kind of business it suits.
What you pay on each payment
Each time a customer pays, the processor keeps a fee and sends you the rest. The fee depends on how the customer pays: by card through the payment link on your invoice, by card in person (tapped, inserted or swiped), by a card you type in yourself (for example over the phone), or by bank transfer straight from their bank account. Square is shown on its free plan, with its paid-plan price in the note.
| When a customer pays by | QuickBooks Payments Built into QuickBooks | Square Free plan | Stripe Standard pricing | PayPal Standard rates | Helcim Price varies by card |
|---|---|---|---|---|---|
What it's built for Ways of selling it has a real product for; the rest work, with limits | Invoices In person, with limits: card reader and Tap to Pay through the QuickBooks app; no point-of-sale system. Online store, with limits: invoices and payment links; works with few shopping carts. | In person, online store and invoices | Online store and invoices In person, with limits: card readers, but no point-of-sale app of its own; you need an app built on Stripe. | In person, online store and invoices | In person and invoices Online store, with limits: its own payment pages; works with only one major shopping cart. |
Card on an invoice or payment page The customer types their card into the page your invoice links to | 2.99% Same price for every card brand, and for PayPal and Venmo | 3.3% + 30¢ 2.9% + 30¢ on Plus or Premium | 2.9% + 30¢ + 0.4% The 0.4% is Stripe Invoicing (Starter), per paid invoice | 2.99% + 49¢ 3.49% + 49¢ when paid with PayPal or Venmo | About 2.31% + 25¢ Helcim's estimate for Visa, Mastercard and Discover; Amex about 2.99% + 25¢. Varies by card |
Card in person Tapped, inserted or swiped on a reader or phone | 2.5% QuickBooks app or GoPayment | 2.6% + 15¢ | 2.7% + 5¢ +10¢ with Tap to Pay; no point-of-sale app of its own | 2.29% + 9¢ PayPal POS app | About 1.79% + 8¢ Visa, Mastercard and Discover; Amex about 2.59% + 8¢, PIN debit about 1.00% + 8¢ |
Card typed in by you You enter the number, for example over the phone | 3.5% | 3.5% + 15¢ | 3.4% + 30¢ Online rate plus 0.5% for manual entry | 3.49% + 9¢ 3.39% + 29¢ through Virtual Terminal | About 2.31% + 25¢ Same as online; Amex about 2.99% + 25¢ |
Bank transfer (ACH) The customer pays from their bank account | 1%, no cap | 1%, $1 minimum No cap on Free; $10 cap on Plus and Premium | 0.8%, up to $5, + 0.4% The 0.4% invoicing fee isn't capped | 1%, up to $10 Pay by Bank on PayPal invoices | 0.5% + 25¢, up to $6 |
Chargeback A customer disputes a card charge with their bank | $25 Plus the disputed amount, held until it's decided | No fee | $15 Another $15 if you contest it manually, refunded if you win | $20 $15 for a PayPal dispute | $15 if you lose $0 if you win |
Card issued outside the US | +1% | +1.5% | +1.5% +1% more if currency is converted | +1.5% | Costs more No fixed add-on; foreign cards carry a higher card cost, passed on to you |
Monthly fee | None Beyond your QuickBooks subscription | None on Free Plus $49, Premium $149 a month | None | None for these products | None |
Your fee when a customer pays a $500 invoice by card What the processor keeps; you receive the rest | $14.95 | $16.80 $14.80 on Plus | $16.80 | $15.44 $17.94 if paid with PayPal or Venmo | About $11.80 At Helcim's estimated rate; about $15.20 with Amex |
Your fee when a customer pays the same $500 invoice by bank transfer Same invoice, paid from the customer's bank account | $5.00 | $5.00 $5.00 on Plus | $6.00 $4.00 bank fee + $2.00 invoicing fee | $5.00 | $2.75 |
Your fee when a customer pays a $1,000 invoice by card What the processor keeps; you receive the rest | $29.90 | $33.30 $29.30 on Plus | $33.30 | $30.39 $35.39 if paid with PayPal or Venmo | About $23.35 At Helcim's estimated rate; about $30.15 with Amex |
Your fee when a customer pays the same $1,000 invoice by bank transfer Same invoice, paid from the customer's bank account | $10.00 | $10.00 $10.00 on Plus | $9.00 $5.00 bank fee + $4.00 invoicing fee | $10.00 | $5.25 |
What it's built for
Ways of selling it has a real product for; the rest work, with limits
QuickBooks Payments
Invoices
In person, with limits: card reader and Tap to Pay through the QuickBooks app; no point-of-sale system. Online store, with limits: invoices and payment links; works with few shopping carts.
Square
In person, online store and invoices
Stripe
Online store and invoices
In person, with limits: card readers, but no point-of-sale app of its own; you need an app built on Stripe.
PayPal
In person, online store and invoices
Helcim
In person and invoices
Online store, with limits: its own payment pages; works with only one major shopping cart.
Card on an invoice or payment page
The customer types their card into the page your invoice links to
QuickBooks Payments
2.99%
Same price for every card brand, and for PayPal and Venmo
Square
3.3% + 30¢
2.9% + 30¢ on Plus or Premium
Stripe
2.9% + 30¢ + 0.4%
The 0.4% is Stripe Invoicing (Starter), per paid invoice
PayPal
2.99% + 49¢
3.49% + 49¢ when paid with PayPal or Venmo
Helcim
About 2.31% + 25¢
Helcim's estimate for Visa, Mastercard and Discover; Amex about 2.99% + 25¢. Varies by card
Card in person
Tapped, inserted or swiped on a reader or phone
QuickBooks Payments
2.5%
QuickBooks app or GoPayment
Square
2.6% + 15¢
Stripe
2.7% + 5¢
+10¢ with Tap to Pay; no point-of-sale app of its own
PayPal
2.29% + 9¢
PayPal POS app
Helcim
About 1.79% + 8¢
Visa, Mastercard and Discover; Amex about 2.59% + 8¢, PIN debit about 1.00% + 8¢
Card typed in by you
You enter the number, for example over the phone
QuickBooks Payments
3.5%
Square
3.5% + 15¢
Stripe
3.4% + 30¢
Online rate plus 0.5% for manual entry
PayPal
3.49% + 9¢
3.39% + 29¢ through Virtual Terminal
Helcim
About 2.31% + 25¢
Same as online; Amex about 2.99% + 25¢
Bank transfer (ACH)
The customer pays from their bank account
QuickBooks Payments
1%, no cap
Square
1%, $1 minimum
No cap on Free; $10 cap on Plus and Premium
Stripe
0.8%, up to $5, + 0.4%
The 0.4% invoicing fee isn't capped
PayPal
1%, up to $10
Pay by Bank on PayPal invoices
Helcim
0.5% + 25¢, up to $6
Chargeback
A customer disputes a card charge with their bank
QuickBooks Payments
$25
Plus the disputed amount, held until it's decided
Square
No fee
Stripe
$15
Another $15 if you contest it manually, refunded if you win
PayPal
$20
$15 for a PayPal dispute
Helcim
$15 if you lose
$0 if you win
Card issued outside the US
QuickBooks Payments
+1%
Square
+1.5%
Stripe
+1.5%
+1% more if currency is converted
PayPal
+1.5%
Helcim
Costs more
No fixed add-on; foreign cards carry a higher card cost, passed on to you
Monthly fee
QuickBooks Payments
None
Beyond your QuickBooks subscription
Square
None on Free
Plus $49, Premium $149 a month
Stripe
None
PayPal
None for these products
Helcim
None
Your fee when a customer pays a $500 invoice by card
What the processor keeps; you receive the rest
QuickBooks Payments
$14.95
Square
$16.80
$14.80 on Plus
Stripe
$16.80
PayPal
$15.44
$17.94 if paid with PayPal or Venmo
Helcim
About $11.80
At Helcim's estimated rate; about $15.20 with Amex
Your fee when a customer pays the same $500 invoice by bank transfer
Same invoice, paid from the customer's bank account
QuickBooks Payments
$5.00
Square
$5.00
$5.00 on Plus
Stripe
$6.00
$4.00 bank fee + $2.00 invoicing fee
PayPal
$5.00
Helcim
$2.75
Your fee when a customer pays a $1,000 invoice by card
What the processor keeps; you receive the rest
QuickBooks Payments
$29.90
Square
$33.30
$29.30 on Plus
Stripe
$33.30
PayPal
$30.39
$35.39 if paid with PayPal or Venmo
Helcim
About $23.35
At Helcim's estimated rate; about $30.15 with Amex
Your fee when a customer pays the same $1,000 invoice by bank transfer
Same invoice, paid from the customer's bank account
QuickBooks Payments
$10.00
Square
$10.00
$10.00 on Plus
Stripe
$9.00
$5.00 bank fee + $4.00 invoicing fee
PayPal
$10.00
Helcim
$5.25
Do bank transfers apply to you?
Bank transfers (also called ACH) are mostly how other businesses pay invoices, and how clients pay large or recurring bills such as retainers. They're much cheaper than cards, but slower to arrive. If your customers almost always pay by card, the bank-transfer row makes little difference to you. If they don't, note that QuickBooks' 1% has no cap, while Helcim, PayPal, Stripe and Square Plus stop at $5 to $10. QuickBooks also lets the client pay a flat $25 for a bank transfer instead, on invoices from $125 to $100,000, if bank transfer is the only payment option on that invoice.
Why Helcim's prices say "about": Helcim passes on each card's own cost, which is lower for debit cards and higher for rewards and business cards, and adds a small published markup. The figures shown are Helcim's own estimate for Visa, Mastercard and Discover. The others charge one flat price whichever card the customer uses. QuickBooks Payments also publishes two discounts: businesses processing over $2,500 a month could qualify for up to 25% off by phone, and clients referred by their accountant get 2.8% on invoice card payments and bank transfers capped at $15.
How each option connects to QuickBooks
When a customer pays, your books need three things: the sale, the processor's fee, and the deposit that later lands in your bank. If all three arrive in QuickBooks on their own, matching your bank account to your books takes minutes. If they don't, you're typing them in by hand.
| QuickBooks Payments Built into QuickBooks | Square Free plan | Stripe Standard pricing | PayPal Standard rates | Helcim Price varies by card | |
|---|---|---|---|---|---|
Who builds the connection | Intuit (built in) | Intuit "Square Connector by QuickBooks" | Third-party apps For example QuickBooks Sync by Acodei | Intuit PayPal connection in QuickBooks bank feeds | Helcim |
Cost | Free | Free for QuickBooks users | $12 or $150 a month By transaction count; 14-day trial | No charge stated | Free |
What reaches QuickBooks | Paid invoices, fees and each day's deposit Matched to your bank feed where your bank supports it | Sales, refunds, fees, taxes and payouts Within a few hours | Sales, refunds, payouts, invoices and fees Sales tax needs Stripe Tax | Every change to your PayPal balance Every 3 hours; fees added when you match, not as separate lines | Payments, back to your QuickBooks invoices Refunds in Helcim don't update the invoice |
Where you send invoices from | QuickBooks | Square The sale is copied into QuickBooks | Stripe, or your own checkout | PayPal | QuickBooks Invoices are copied to Helcim, which collects the payment |
Who builds the connection
QuickBooks Payments
Intuit (built in)
Square
Intuit
"Square Connector by QuickBooks"
Stripe
Third-party apps
For example QuickBooks Sync by Acodei
PayPal
Intuit
PayPal connection in QuickBooks bank feeds
Helcim
Helcim
Cost
QuickBooks Payments
Free
Square
Free for QuickBooks users
Stripe
$12 or $150 a month
By transaction count; 14-day trial
PayPal
No charge stated
Helcim
Free
What reaches QuickBooks
QuickBooks Payments
Paid invoices, fees and each day's deposit
Matched to your bank feed where your bank supports it
Square
Sales, refunds, fees, taxes and payouts
Within a few hours
Stripe
Sales, refunds, payouts, invoices and fees
Sales tax needs Stripe Tax
PayPal
Every change to your PayPal balance
Every 3 hours; fees added when you match, not as separate lines
Helcim
Payments, back to your QuickBooks invoices
Refunds in Helcim don't update the invoice
Where you send invoices from
QuickBooks Payments
QuickBooks
Square
Square
The sale is copied into QuickBooks
Stripe
Stripe, or your own checkout
PayPal
PayPal
Helcim
QuickBooks
Invoices are copied to Helcim, which collects the payment
Where you send invoices from matters
When a customer pays a QuickBooks invoice online, QuickBooks Payments processes it. With Square, Stripe or PayPal you usually send the invoice from that processor instead, and the connection copies the sale into QuickBooks. If you live in QuickBooks invoicing, that's a change to how you work, not just a different fee. Helcim is the exception: it copies your QuickBooks invoices across and collects the payment.
How long until the money is in your bank
A paid invoice isn't money in your bank yet. Each processor sends what it collected to your business bank account as a deposit. The standard deposit is free and takes one or more business days; most also sell an instant deposit, within minutes, for a fee. Bank transfers take longer to clear than cards, new accounts wait longest while the processor reviews them, and weekends don't count, so four or five business days is easy to hit.
| Payment type | QuickBooks Payments Built into QuickBooks | Square Free plan | Stripe Standard pricing | PayPal Standard rates | Helcim Price varies by card |
|---|---|---|---|---|---|
Card payments Standard deposit, free | Next business day if paid before 3 PM PT Another section of the same Intuit article says 2 business days | Next business day if paid before 5 PM PT Later payments: by the second business day | 2 business days Your bank may take longer to release it | In your PayPal balance within minutes; to your bank in about 1 business day (up to 3) Moving money from PayPal to your bank is free; after 7 PM ET or on weekends, add a day | 1 to 2 business days after the day's batch closes Next business day, free, if your bank is on RTP or FedNow |
Bank-transfer payments These take longer than cards to clear | Next business day, like cards Slower during your first month | Not stated Square says bank payments follow your deposit schedule once they clear | Up to 4 business days to clear, then paid out on your schedule | Not stated for invoice Pay by Bank | 3 to 5 business days |
Your first deposits New accounts are reviewed first | Within 5 business days | Not stated | 7 to 14 days after your first payment | No fixed delay; holds on new sellers generally up to 21 days | About 3 business days for cards, about 7 for bank payments |
Weekends and holidays | Deposits Monday to Saturday Not on Sundays or federal holidays | No Saturday transfers Friday's money stays in your Square balance over the weekend unless you change the setting | Business days only A Saturday payment starts counting on Monday | Business days only | Business days only A batch closed Friday evening starts counting on Monday |
Instant deposit Optional, for a fee | 1.75%, any day Free for eligible payments into QuickBooks Checking | 1.95%, any day Same-day transfer also 1.95% | 1.5%, 50¢ minimum New accounts aren't eligible right away | 1.5%, 50¢ minimum; arrives in minutes | Not offered |
Card payments
Standard deposit, free
QuickBooks Payments
Next business day if paid before 3 PM PT
Another section of the same Intuit article says 2 business days
Square
Next business day if paid before 5 PM PT
Later payments: by the second business day
Stripe
2 business days
Your bank may take longer to release it
PayPal
In your PayPal balance within minutes; to your bank in about 1 business day (up to 3)
Moving money from PayPal to your bank is free; after 7 PM ET or on weekends, add a day
Helcim
1 to 2 business days after the day's batch closes
Next business day, free, if your bank is on RTP or FedNow
Bank-transfer payments
These take longer than cards to clear
QuickBooks Payments
Next business day, like cards
Slower during your first month
Square
Not stated
Square says bank payments follow your deposit schedule once they clear
Stripe
Up to 4 business days to clear, then paid out on your schedule
PayPal
Not stated for invoice Pay by Bank
Helcim
3 to 5 business days
Your first deposits
New accounts are reviewed first
QuickBooks Payments
Within 5 business days
Square
Not stated
Stripe
7 to 14 days after your first payment
PayPal
No fixed delay; holds on new sellers generally up to 21 days
Helcim
About 3 business days for cards, about 7 for bank payments
Weekends and holidays
QuickBooks Payments
Deposits Monday to Saturday
Not on Sundays or federal holidays
Square
No Saturday transfers
Friday's money stays in your Square balance over the weekend unless you change the setting
Stripe
Business days only
A Saturday payment starts counting on Monday
PayPal
Business days only
Helcim
Business days only
A batch closed Friday evening starts counting on Monday
Instant deposit
Optional, for a fee
QuickBooks Payments
1.75%, any day
Free for eligible payments into QuickBooks Checking
Square
1.95%, any day
Same-day transfer also 1.95%
Stripe
1.5%, 50¢ minimum
New accounts aren't eligible right away
PayPal
1.5%, 50¢ minimum; arrives in minutes
Helcim
Not offered
Plan your cash around the slowest case, especially in your first weeks with a processor. Instant deposit only speeds up the last step; it doesn't make a bank transfer clear any faster.
Bottom line: which option fits your business
Based on the published prices, deposit times and QuickBooks connections above. A quote for your own account can differ.
| If your business | Best fit | Why |
|---|---|---|
| Invoices from QuickBooks, and clients mostly pay by card | QuickBooks Payments | The lowest flat price on invoice card payments at every size we checked: 2.99% with no fixed fee, with Amex, PayPal and Venmo at the same price. Nothing to connect, and deposits the next business day. |
| Mostly small payments, under about $100 | QuickBooks Payments | With no fixed fee per payment, it costs least of the flat-rate options on small amounts: $1.50 on a $50 card payment, against $1.95 at Square, $1.95 at Stripe and $1.99 at PayPal. |
| Clients often pay by bank transfer, on invoices over about $1,000 | Helcim, or PayPal | QuickBooks' 1% bank fee has no cap. Helcim's stops at $6, the lowest here; PayPal's at $10 (cheaper than Stripe above about $1,250). Or stay with QuickBooks Payments and have the client pay its flat $25 bank-transfer fee. |
| You want the lowest card cost, and a price that varies by card is fine | Helcim | Its own estimate is about 2.31% + 25¢ on invoice card payments and 1.79% + 8¢ in person, below every flat price here, and it lets you keep invoicing from QuickBooks. No instant deposit, and first deposits take a few extra days. |
| You also sell in person (a counter, events, appointments) | Square, or QuickBooks Payments | Square's free point-of-sale app and Intuit's free Square connector suit a shop counter (2.6% + 15¢). For the occasional in-person payment, QuickBooks Payments' 2.5% through the QuickBooks app or GoPayment avoids a second system. |
| You sell online or need a custom checkout | Stripe | Built for online checkout at 2.9% + 30¢ per card payment. Budget for a sync app (from $12 a month) and expect a 7 to 14 day wait for your first payout. |
| Your customers like paying with PayPal or Venmo | QuickBooks Payments | A QuickBooks invoice already accepts PayPal and Venmo at 2.99%. PayPal's own invoices charge 3.49% + 49¢ when the customer pays that way. |
| Cash flow is tight | QuickBooks Payments or Square | Both deposit card payments the next business day if paid before their cutoff, and both offer instant deposits (QuickBooks waives its 1.75% fee into QuickBooks Checking). |
Invoices from QuickBooks, and clients mostly pay by card
Best fit: QuickBooks Payments
Why: The lowest flat price on invoice card payments at every size we checked: 2.99% with no fixed fee, with Amex, PayPal and Venmo at the same price. Nothing to connect, and deposits the next business day.
Mostly small payments, under about $100
Best fit: QuickBooks Payments
Why: With no fixed fee per payment, it costs least of the flat-rate options on small amounts: $1.50 on a $50 card payment, against $1.95 at Square, $1.95 at Stripe and $1.99 at PayPal.
Clients often pay by bank transfer, on invoices over about $1,000
Best fit: Helcim, or PayPal
Why: QuickBooks' 1% bank fee has no cap. Helcim's stops at $6, the lowest here; PayPal's at $10 (cheaper than Stripe above about $1,250). Or stay with QuickBooks Payments and have the client pay its flat $25 bank-transfer fee.
You want the lowest card cost, and a price that varies by card is fine
Best fit: Helcim
Why: Its own estimate is about 2.31% + 25¢ on invoice card payments and 1.79% + 8¢ in person, below every flat price here, and it lets you keep invoicing from QuickBooks. No instant deposit, and first deposits take a few extra days.
You also sell in person (a counter, events, appointments)
Best fit: Square, or QuickBooks Payments
Why: Square's free point-of-sale app and Intuit's free Square connector suit a shop counter (2.6% + 15¢). For the occasional in-person payment, QuickBooks Payments' 2.5% through the QuickBooks app or GoPayment avoids a second system.
You sell online or need a custom checkout
Best fit: Stripe
Why: Built for online checkout at 2.9% + 30¢ per card payment. Budget for a sync app (from $12 a month) and expect a 7 to 14 day wait for your first payout.
Your customers like paying with PayPal or Venmo
Best fit: QuickBooks Payments
Why: A QuickBooks invoice already accepts PayPal and Venmo at 2.99%. PayPal's own invoices charge 3.49% + 49¢ when the customer pays that way.
Cash flow is tight
Best fit: QuickBooks Payments or Square
Why: Both deposit card payments the next business day if paid before their cutoff, and both offer instant deposits (QuickBooks waives its 1.75% fee into QuickBooks Checking).
To price your own mix of invoices and in-person sales, use the credit card processing fee calculator.
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