Sync Invoices with QuickBooks

How invoices sync from JobsiteOn to QuickBooks Online and how payments, refunds and voids sync both ways, including which fields map and how to handle errors.

Written by Ethan RiveraUpdated over a week ago23 min readBeginner

What this guide covers

This guide explains how invoices sync from JobsiteOn to QuickBooks Online and how payments sync both ways. You will learn which invoice fields map to QuickBooks, when the sync triggers, and how to resolve common sync errors.

Before you begin

QuickBooks Online must be connected. See Connect QuickBooks Online.
Invoices must be turned on under Sync settings on the QuickBooks page.

How invoice sync works

Invoice sync is one-directional: JobsiteOn pushes invoices to QuickBooks. Invoices created in QuickBooks are not pulled into JobsiteOn.

Editing a synced invoice in QuickBooks doesn't change it in JobsiteOn. JobsiteOn stays the source for invoice details, so your next edit in JobsiteOn replaces the QuickBooks version. Payments recorded in QuickBooks still update the invoice balance in JobsiteOn.

JobsiteOn field	QuickBooks field
Invoice Number	Doc Number
Customer	Customer Ref
Issue Date	Invoice Date
Due Date	Due Date
Line Items	Line Items
Discount	Discount Line
Tax	Not sent (QuickBooks calculates it)
Total	N/A (calculated)
Status	N/A (calculated)

The customer on the QuickBooks invoice is the job's customer contact. If that contact isn't in QuickBooks yet, JobsiteOn sends it first.

Screenshot: A JobsiteOn invoice detail page with an annotation showing which fields map to QuickBooks and a "Synced" badge in the corner.

When invoices sync

Automatic: when you create or edit an invoice, cancel it, or mark it paid, the change goes to QuickBooks within a few minutes. New invoices start as drafts in JobsiteOn, and a draft goes to QuickBooks as soon as it's created, before you send it to your customer.
Cancelled invoices: cancelling an invoice in JobsiteOn voids it in QuickBooks. A payment JobsiteOn had sent that was refunded in full, or that bounced, is voided in QuickBooks too, even if the invoice was cancelled before that change reached QuickBooks. Payments on it that never reached QuickBooks aren't sent once it's cancelled.
Existing invoices: when you connect or reconnect, and each time you click Sync now, JobsiteOn queues invoices that never reached QuickBooks, except drafts and cancelled invoices.
Same invoice number: if QuickBooks already has an invoice with the same number when JobsiteOn first sends one, JobsiteOn links to it and replaces its details with the JobsiteOn invoice. For the payments on it, see "Which payments go to QuickBooks" and "Invoice taken over by number" below.

Payment sync

Payments sync both ways when Payments sync is turned on for QuickBooks: payments recorded in JobsiteOn go to QuickBooks, and payments recorded in QuickBooks come into JobsiteOn.

JobsiteOn treats a JobsiteOn payment and a QuickBooks payment as the same payment when JobsiteOn sent it to QuickBooks itself (its QuickBooks memo starts with "Recorded in JobsiteOn"), the two are already linked, you chose Same payment for them on the sync errors page, or they plainly match: the same amount on the same invoice, dated at most 3 days apart, with no other payment they could be (see "Possible duplicate payment" below). When it isn't that clear, JobsiteOn asks you.

From JobsiteOn to QuickBooks

When you record a payment in JobsiteOn, or a customer pays online, JobsiteOn adds the payment in QuickBooks and applies it to the same invoice, so the payment shows on the invoice there too. The payment keeps its date, amount, and reference or check number. If the invoice isn't in QuickBooks yet, JobsiteOn sends the invoice first (when Invoices sync is on).

Which payments go to QuickBooks: JobsiteOn sends a payment when any of these is true:
- It was recorded while Payments sync was on. Payments sync starts when you connect, and starts again each time you turn the Payments switch back on, or connect again after a disconnect. Turning the switch off, or disconnecting, stops it. Reconnecting after QuickBooks sync was paused or needed reconnecting doesn't change it. A payment counts from when it was entered in JobsiteOn or from its payment date, whichever is later.
- JobsiteOn itself added its invoice to QuickBooks while Payments sync was on, since QuickBooks had no payments on that invoice. If JobsiteOn added it after Payments sync last started, all of its payments go. If it added it during the previous time Payments sync was on, the payments recorded before Payments sync was turned off or QuickBooks was disconnected go, but not ones recorded while it was off. An invoice JobsiteOn took over because QuickBooks already had its number doesn't count as added, unless QuickBooks created that invoice after you first connected and shows nothing paid on it, such as one JobsiteOn itself sent on an earlier try that QuickBooks didn't confirm.
- You chose Different payments for it on a possible duplicate warning (see "Possible duplicate payment" below). That sends the JobsiteOn payments the warning names, even if the two rules above would hold them back. One that another open possible duplicate on the same invoice also names waits until no open warning names it.
Other payments: any other payment, such as one recorded before you first connected, or while Payments sync was off or QuickBooks was disconnected, isn't sent, so a payment you already entered in QuickBooks isn't recorded twice. Later changes to it, such as a refund, aren't sent either. You see the sync error "Payments recorded before Payments sync was turned on were not sent to QuickBooks." If one of those payments is missing in QuickBooks, record it there yourself for the same amount on the same invoice. JobsiteOn then shows a possible duplicate warning. If the JobsiteOn invoice still shows money owed, JobsiteOn brings that QuickBooks payment in first. If it already shows paid in full, JobsiteOn doesn't bring it in, but still shows the warning. Either way, choose Same payment there (see "Possible duplicate payment" below): JobsiteOn links the two, so each system counts the payment once and later refunds reach QuickBooks. If Payments sync starts again later and more payments are left out, JobsiteOn marks the earlier error resolved and shows a new one.
Turning Payments sync off and on: while Payments sync is off, no payment changes go to QuickBooks. When you turn it back on, the changes made in the meantime to payments JobsiteOn had already sent, such as refunds, go out within a few minutes, without Sync now. So do payments that were due to go when you turned it off but hadn't reached QuickBooks yet, if their invoice is already there: ones recorded while it was on, and ones on an invoice JobsiteOn added to QuickBooks while it was on. Otherwise they go with the invoice when it's sent. JobsiteOn remembers only the most recent time Payments sync was on before the current one, so a payment that still hasn't gone by the next time it's turned off or QuickBooks is disconnected isn't sent after that. Payments recorded while it was off are other payments, as described above.
More than the QuickBooks invoice has open: JobsiteOn doesn't send tax, so a QuickBooks invoice can total less than the JobsiteOn invoice. Before adding a payment, JobsiteOn reads the QuickBooks invoice. It still records the whole payment in QuickBooks, but applies only what the invoice has open there and leaves the rest as a credit for the customer. You see the sync error "A payment recorded in JobsiteOn was more than the invoice had open in QuickBooks." If the QuickBooks invoice should match JobsiteOn, correct it in QuickBooks and apply the customer's credit to it.
Credit you applied by hand: when JobsiteOn later updates such a payment, for example after a refund, it keeps the credit you applied in QuickBooks, whether to this invoice or another one. If a change, such as a partial refund, would leave the payment smaller than what it applies to other invoices, JobsiteOn doesn't change it and shows the sync error "A payment change was not sent because QuickBooks applies part of that payment to other invoices." In QuickBooks, lower what the payment applies to other invoices to the amount the error names, then click Sync now. A change that leaves nothing of the payment, such as a full refund on a partly paid invoice, still voids the whole QuickBooks payment, including what it applies to other invoices.
Invoice taken over by number: QuickBooks may already have payments on an invoice JobsiteOn took over because it had the same number. JobsiteOn leaves them alone: a QuickBooks payment created before JobsiteOn took the invoice over doesn't come into JobsiteOn, even if it's applied to the invoice later, and it never raises a possible duplicate warning. Payments entered in QuickBooks after that come in as usual. JobsiteOn doesn't look for a matching payment before it sends its own, so a JobsiteOn payment that's due to go (see "Which payments go to QuickBooks") is added in QuickBooks even when one for the same amount is already there. If the QuickBooks invoice has less open than the payment, the rest is left as a customer credit with the sync error "A payment recorded in JobsiteOn was more than the invoice had open in QuickBooks." Otherwise no sync error shows. If you entered a payment only in QuickBooks before JobsiteOn took the invoice over, JobsiteOn doesn't show it and still counts that amount as owed. Don't record it again in JobsiteOn, because JobsiteOn would send that copy to QuickBooks too. Use Contact support in the Help menu instead.
Payment entered in both places: record each payment in one place when you can. If a payment recorded in JobsiteOn is also entered by hand in QuickBooks, what happens depends on whether JobsiteOn's payment is in QuickBooks yet:
- JobsiteOn hasn't sent its payment: when the two amounts match, JobsiteOn shows a possible duplicate warning and you decide in JobsiteOn with Same payment or Different payments (see "Possible duplicate payment" below). If the JobsiteOn invoice still shows money owed, the QuickBooks payment comes in first. If it already shows paid in full, the QuickBooks payment doesn't come in. Answer soon: a JobsiteOn payment that's due to go, such as one waiting to go or one QuickBooks turned down, can still reach QuickBooks before you answer, and then it's the next case.
- JobsiteOn's payment is in QuickBooks too: both payments are then in QuickBooks, and no possible duplicate warning shows. If the QuickBooks invoice still had that much open, JobsiteOn's payment was applied to it in full. If it had less open, the rest was left as a customer credit with the sync error "A payment recorded in JobsiteOn was more than the invoice had open in QuickBooks." The one entered in QuickBooks can also come into JobsiteOn whenever the JobsiteOn invoice has money owed. Because JobsiteOn's payment is already in QuickBooks, the fix is in QuickBooks, not on the sync errors page: void or delete the payment you entered by hand there, not the one JobsiteOn sent, whose memo starts with "Recorded in JobsiteOn". If JobsiteOn brought the other payment in, it takes it off the invoice too. Voiding it doesn't move JobsiteOn's payment onto the invoice, so if part or all of JobsiteOn's payment was left as a customer credit, apply that credit to the invoice in QuickBooks. Then check that the invoice shows the same amount owed in both systems.
While syncing is stopped: payments recorded, refunded or deleted while QuickBooks sync was paused or needed reconnecting go to QuickBooks when syncing starts again, if their invoice is already there. Otherwise they go with the invoice when you reconnect or click Sync now.
After you disconnect: payments recorded while QuickBooks was disconnected aren't sent when you connect again, except on invoices JobsiteOn adds to QuickBooks after that, or when you choose Different payments for one. Changes made in the meantime to payments JobsiteOn had already sent, such as refunds, go out when you reconnect, and so do payments that were due to go before the disconnect but hadn't reached QuickBooks yet: ones recorded while Payments sync was on, and ones on an invoice JobsiteOn added to QuickBooks while it was on.
Refund on an invoice paid in full: JobsiteOn keeps the invoice settled, so the QuickBooks payment stays as it is and the invoice stays paid in QuickBooks too. Nothing about the refund goes to QuickBooks. You see the sync error "A refund recorded in JobsiteOn was not sent to QuickBooks." Record the refund in QuickBooks yourself, for example as a refund receipt. A lost chargeback on an invoice paid in full works the same way.
Refund on a partly paid invoice: the balance opens again in JobsiteOn, so JobsiteOn lowers the QuickBooks payment to what's left. A full refund voids it, even if you then cancel the invoice.
Bounced bank payment: a bank payment that bounces voids the payment in QuickBooks, and the invoice opens back up in both places.
Still processing or disputed: online payments that are still processing wait until they clear. A payment under dispute stays as it is in QuickBooks until the dispute is decided.

From QuickBooks to JobsiteOn

When a payment is recorded in QuickBooks against a synced invoice, it comes into JobsiteOn and updates the invoice balance, up to what the JobsiteOn invoice still has open. A credit memo applied to a synced invoice in QuickBooks comes in the same way. If that payment or credit is later voided or deleted in QuickBooks, JobsiteOn takes it off the invoice, and the invoice opens back up with its balance due. Other payments on the invoice aren't touched. On an invoice JobsiteOn took over by number, QuickBooks payments created before it took the invoice over don't come in (see "Invoice taken over by number" above). If the invoice also has a JobsiteOn payment for the same amount that JobsiteOn hasn't sent, see "Possible duplicate payment" below.

JobsiteOn usually hears about these changes within a few minutes. If it misses one, Sync now usually catches it. A delete older than 30 days can't be caught.

When a QuickBooks payment applies more than the JobsiteOn invoice has open, for example because the invoice already shows paid in JobsiteOn, JobsiteOn brings in only what fits, or nothing, and notes the rest. Once the invoice has money owed again, JobsiteOn rechecks that invoice's payments in QuickBooks and brings in what now fits, up to what's owed. The recheck runs right after you answer a possible duplicate, and within a few minutes when the invoice opens up in another way, such as when a payment JobsiteOn brought in from QuickBooks is voided or deleted there. Each backup check and Sync now also rechecks up to 25 invoices that have such a payment and money owed. If a QuickBooks payment still hasn't come in once the JobsiteOn invoice shows money owed, open it in QuickBooks and save it again, and JobsiteOn reads it again. A payment created before JobsiteOn took its invoice over by number stays out.

Note: A payment JobsiteOn sent to QuickBooks is never copied back into JobsiteOn as a second payment. If someone voids or deletes it inside QuickBooks, JobsiteOn keeps it and shows a sync error, so you can decide which side is right. The same goes for lowering it in QuickBooks, moving it to another invoice, or leaving it unapplied as a customer credit: JobsiteOn keeps its amount and shows the sync error "A payment recorded in JobsiteOn was changed in QuickBooks." A QuickBooks payment you linked with Same payment is handled the same way.

Payment recorded in QuickBooks without an invoice

Sometimes a customer's payment is recorded in QuickBooks without picking the invoice it pays, so QuickBooks keeps it as a credit for the customer. JobsiteOn matches it to your invoice on its own when all of this is true:

The QuickBooks customer is the invoice's customer in JobsiteOn.
The payment is exactly what the invoice still has due.
The invoice was sent (not a draft) and is still open.
The payment is dated from 7 days before the invoice was sent to 120 days after.
No other open invoice of that customer matches the same way, and the invoice has no JobsiteOn payment of that amount that JobsiteOn hasn't sent to QuickBooks yet.

JobsiteOn then marks the invoice paid and applies the payment to the same invoice in QuickBooks, so both show it paid. If QuickBooks shows less open on that invoice than the payment (usually sales tax), JobsiteOn still marks the invoice paid but leaves the payment unapplied in QuickBooks, and the sync errors page asks you to apply it there.

If the payment matches more than one open invoice, JobsiteOn doesn't guess. The sync errors page lists the invoices it could pay. Apply the payment to the right invoice in QuickBooks and JobsiteOn marks that invoice paid on the next sync. A payment you later apply to a different invoice in QuickBooks moves to that invoice in JobsiteOn too.

Possible duplicate payment

Say a payment comes in from QuickBooks on an invoice that also has a JobsiteOn payment for exactly the same amount that JobsiteOn hasn't sent to QuickBooks: one held back because of when it was recorded, one waiting to go, one QuickBooks turned down, or one whose send QuickBooks never confirmed. JobsiteOn doesn't guess whether they're one payment recorded in both places or two different payments, such as two equal installments. It shows a warning on the sync errors page and asks you.

The other way around works too: if the same payment is already in QuickBooks when JobsiteOn sends its own (same customer, exactly the same amount on that invoice, dated at most 3 days apart), JobsiteOn links to it instead of adding a second payment in QuickBooks.

When the match is plain, JobsiteOn answers Same payment for you within a few minutes: the invoice has exactly one such JobsiteOn payment, it was never refunded, it is dated at most 3 days from the QuickBooks payment, and the QuickBooks payment pays only this invoice. The warning then shows as resolved with "Matched automatically". Equal installments recorded further apart still wait for your answer. While the warning is open, the QuickBooks page shows the banner "A QuickBooks payment may be counted twice" with a View sync errors link.

If the JobsiteOn invoice still shows money owed, JobsiteOn brings the QuickBooks payment in and counts both until you answer. The warning reads "A payment imported from QuickBooks may already be recorded in JobsiteOn."
If the JobsiteOn invoice already shows paid in full, JobsiteOn doesn't bring the QuickBooks payment in. The warning reads "A payment recorded in QuickBooks may already be recorded in JobsiteOn.", because if JobsiteOn sent its own payment too, QuickBooks would count the money twice. In the Match the QuickBooks payment window, that payment shows as not brought in to JobsiteOn.
The JobsiteOn payment has to have cleared. One that was partly refunded counts as the same amount when the QuickBooks payment matches either its original amount or what's left after the refund. One refunded in full never matches.
JobsiteOn compares the full amount the QuickBooks payment applies to the invoice, even when it brought in less because that was all the invoice had open.
The warning names the QuickBooks payment, its amount, the invoice and the JobsiteOn payment. It shows once for each QuickBooks payment and invoice. Once you answer it, JobsiteOn doesn't ask again about that QuickBooks payment on that invoice, even if it brings the payment in later. A JobsiteOn payment it names stays a match until it's refunded in full, removed or sent, even if a later partial refund changes its amount.

The warning has two buttons instead of Mark Resolved:

Same payment: for one payment recorded in both places. In the Match the QuickBooks payment window, pick the JobsiteOn payment that's the same money, then click Link payments. JobsiteOn first reads the QuickBooks payment as it is in QuickBooks right now. It then links your payment to the QuickBooks payment, removes the copy it brought in, if there is one, and updates the invoice balance, so JobsiteOn and QuickBooks each count the money once, even if JobsiteOn had brought in less than the full amount. From then on that QuickBooks payment belongs to your JobsiteOn payment, as if JobsiteOn had sent it: JobsiteOn applies your refunds and voids to it by the rules above, and never adds a second QuickBooks payment for it. When the amounts already match, nothing changes in QuickBooks. When the payment you pick holds a different amount, for example after a partial refund, the window says so, and JobsiteOn's next payment sync updates the QuickBooks payment the same way it handles any refund (see "Refund on an invoice paid in full" and "Refund on a partly paid invoice" above). If QuickBooks never confirmed an earlier send of your payment and that send did land, JobsiteOn finds it and voids it.

Same payment works only when the QuickBooks payment pays this one invoice and leaves no credit. Otherwise JobsiteOn shows a message and changes nothing. You can change the payment in QuickBooks so it pays only this invoice and then click Same payment again, or choose Different payments. If the QuickBooks payment was voided or deleted in QuickBooks, JobsiteOn says there's nothing to link, and the warning resolves itself with the next sync. If JobsiteOn can't read QuickBooks right then, or is syncing payments with QuickBooks at that moment, it asks you to try again in a minute.
Different payments: for two separate payments. JobsiteOn asks you to confirm and names the JobsiteOn payments on the warning, with their amounts. When it brought the QuickBooks payment in, it asks "Keep both payments?" and you click Keep both. When it didn't, because the JobsiteOn invoice already shows paid in full, it asks "Treat them as different payments?" and you click Different payments. JobsiteOn then:
- leaves the QuickBooks payment as it is. A copy it brought in stays in JobsiteOn. One it didn't bring in stays out of JobsiteOn until the invoice has money owed again (see "From QuickBooks to JobsiteOn" above).
- sends to QuickBooks each JobsiteOn payment the warning names that it hasn't sent yet and that still holds money, even if "Which payments go to QuickBooks" above would hold it back. Each is sent like any other payment JobsiteOn sends.
- holds back, for now, a payment that another open possible duplicate on the same invoice also names, because it may still be that other QuickBooks payment. JobsiteOn sends it once no open warning names it, unless you link it with Same payment there, or it's refunded in full, removed or sent first. A payment that was due to go anyway, such as one waiting to go, still goes on its usual schedule.
A message then names the payments JobsiteOn is sending. When JobsiteOn didn't bring the QuickBooks payment in, the message starts "Marked as different payments. JobsiteOn brings the QuickBooks payment in only when the invoice has money owed in JobsiteOn." When you check Show resolved, a resolved entry for each payment says JobsiteOn is sending it. If the QuickBooks invoice has less open than a payment, the rest is left as a customer credit with the sync error "A payment recorded in JobsiteOn was more than the invoice had open in QuickBooks." For a payment sent because you chose Different payments, that error's hint says so and that the credit is expected when the customer paid twice. It tells you to refund the credit in QuickBooks or apply it to another invoice for that customer, and not to raise the invoice total to use it up.

Right after either answer, JobsiteOn rechecks the invoice's payments in QuickBooks and brings in any that now fit, such as one it left out while the invoice counted the same money twice.

The warning also resolves itself, with no button to click, when:

the QuickBooks payment is voided or deleted in QuickBooks, or taken off the invoice there. JobsiteOn removes the copy it brought in, if there is one, so nothing counts twice.
the JobsiteOn payment is refunded in full.
the JobsiteOn payment reaches QuickBooks before you decide, for example one that was waiting to go. Both payments are then in QuickBooks. If they're the same payment, fix it in QuickBooks as described under "Payment entered in both places" above.

When the warning names more than one JobsiteOn payment, it resolves itself only once none of them is still a match.

If the warning no longer applies when you click Same payment or Different payments, for example because JobsiteOn already took the QuickBooks payment off the invoice after a void in QuickBooks, JobsiteOn says so, doesn't change any payment and updates the list.

Animation: An invoice being created in JobsiteOn, syncing to QuickBooks with a progress animation, and then a payment recorded in QuickBooks pulling back into JobsiteOn.

Common sync errors

Invoice total mismatch

JobsiteOn doesn't send tax. QuickBooks works out the tax on the invoice from its own settings, so the totals differ when those settings don't match the tax you charge in JobsiteOn. Line item rounding can also differ. Check both systems and align the tax settings. When the QuickBooks invoice totals less, a payment for the full JobsiteOn amount leaves the difference as a customer credit in QuickBooks (see "More than the QuickBooks invoice has open" above).

Customer is inactive in QuickBooks

QuickBooks doesn't delete customers. It makes them inactive. If an invoice for an inactive customer fails, make the customer active again in QuickBooks, then click Retry on the failed invoice in the Dead letter queue tab of the sync errors page, or save the invoice again in JobsiteOn.

Duplicate invoice number

JobsiteOn doesn't add a second invoice with a number QuickBooks already has. It takes over the existing QuickBooks invoice and replaces its details. Payments already on it in QuickBooks don't come into JobsiteOn (see "Invoice taken over by number" above). If that QuickBooks invoice wasn't the same sale, change the invoice number in QuickBooks before you connect or before the JobsiteOn invoice is sent.

Tip: Use the sync log to monitor invoice sync status. Check it weekly to catch errors early before they affect your accounting.

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