Prerequisites
Confirm the following before connecting Paychex Flex:- Admin access to both your DualEntry and Paychex Flex accounts.
- Your chart of accounts in DualEntry includes the GL accounts you intend to use for payroll expense, tax expense, employee and employer benefit accounts, and a payroll clearing or accrued-payroll account.
- A vendor record in DualEntry to use as the payroll vendor (typically named “Paychex”).
- A single DualEntry company that the Paychex Flex data should post to. Consolidated payroll runs in single-entity mode only (see Current limitations).
- No classification setup is required in advance. DualEntry splits pay statement lines by Department and Location classifications automatically, creating them on first sync if they do not already exist.
How to connect
DualEntry connects to Paychex Flex through a hosted Connect widget, so you do not generate API keys or paste credentials into DualEntry. The payroll-data provider handles authentication and returns an access token to DualEntry.- In DualEntry, navigate to Company → Integrations → Paychex Flex.
- Choose Connect. DualEntry opens the Connect widget in a new window.
- In the widget, choose Paychex Flex and sign in with your Paychex admin credentials.
- Approve the data scopes requested on DualEntry’s behalf.
- After approval, the provider redirects back to DualEntry and the integration shows as Connected.
What syncs
The integration pulls the following Paychex Flex data into DualEntry on each sync run. Paychex is the system of record; DualEntry ingests this data and does not push anything back.
Pay groups, individuals, entities, and headcount are also pulled by the provider but hidden from the configuration UI for consolidated payroll. They are internal references the integration uses, not records you map.
Map your Paychex Flex data
After connecting, DualEntry pulls Paychex Flex metadata and shows you what to map. Until every required mapping is filled in, the integration shows as not yet set up and pay statements do not post. The mapping work breaks into three pieces. First, map the Paychex company and the payroll vendor so DualEntry knows where journal entries land and which vendor to stamp on every line. Second, map every pay statement item to a GL account so each earnings, tax, deduction, and contribution line posts to the right place. Third, optionally map departments to classifications if you want journal entry lines split by department.Map companies and the payroll vendor
Map the Paychex company to the DualEntry company that should receive the payroll journal entries, and map the payroll vendor to a DualEntry vendor record. The company mapping determines which DualEntry company the consolidated journal entry posts to. The payroll vendor mapping determines the vendor stamped on every line of the journal entry.- Open Company → Integrations → Paychex Flex → Configuration.
- On the Companies tab, map the Paychex company to a single DualEntry company.
- On the Payroll vendor tab, map the Paychex-named vendor to your DualEntry payroll vendor record.
Map pay statement items to GL accounts
Each pay statement item (earnings line, tax line, employee deduction, employer contribution) must map to a DualEntry GL account before pay statements can post.- Open the Pay statement items tab. Items are grouped by category:
earnings,taxes,employee_deductions,employer_contributions. - For each item, choose the DualEntry GL account the line should post to. Item display names follow the pattern
{category}{-Employer|-Employee}: {item name}, for exampletaxes: Federal Income Taxoremployer_contributions-Employer: 401(k) Match. - Confirm the debit/credit direction stored on each item. This controls whether the amount posts as a debit or credit on the journal entry.
Map departments to classifications
Paychex departments sync into a Department classification in DualEntry automatically. DualEntry auto-creates the classification and a line for each department if they do not already exist, then applies them to the journal entry via the saved mapping. This step is optional and needs no per-department setup. If you unmap a department, or remove its classification line, that department is omitted from the journal entry, with no error, and it is not re-created on the next sync.How payroll runs become journal entries
Once setup is complete, each Paychex Flex payment (pay run) becomes a single consolidated journal entry in DualEntry, not one journal entry per employee. The consolidation rules:- All pay statements that share a
payment_idgroup together. - For each unique combination of (pay statement item, classification), the integration sums amounts across employees and creates one journal entry line. For example, with eight departments and a “Salary” item, the entry has eight “Salary” lines, one per department.
- Tax items are grouped by item only, with no classification split. When Consolidate payroll tax is on, tax items are further consolidated by GL account into a single “Consolidated Payroll Tax” line per account.
- The journal entry is dated the payment’s pay date.
- The memo follows the pattern
[Paychex Flex] Payroll {start_date} to {end_date} paid on {pay_date} ({n} employees).
Optional: Consolidate payroll tax
By default, every tax item across a payroll run is consolidated by GL account into a single “Consolidated Payroll Tax” line per account on the journal entry. This keeps the entry compact when many tax types map to the same account, for example several state-specific income taxes all posting to the same expense account. If you would rather see one journal entry line per tax item, for granular reporting or tax-type-level analysis, turn this off:- Open Company → Integrations → Paychex Flex → Settings.
- Toggle Consolidate payroll tax off.
- The next sync re-renders pay statements with one line per (tax item, account).
Current limitations
The Paychex Flex integration has the following limitations today:- Single-entity mode only. Consolidated payroll requires a single DualEntry company per Paychex Flex connection. Multi-entity setups (one connection mapping pay statements to multiple DualEntry companies) are not yet supported and skip pay statement processing with a warning.
- No retroactive remapping. Pay statements already consolidated into a journal entry do not re-post if you later change a pay statement item mapping. Resync the affected payment range to apply the new mapping.
- Department and location classification splits only. Pay statement classification splits use the configured department and location classifications. Splits by other classifications (such as project or class) are not applied automatically.
- Departments match by exact name. A Paychex department reuses an existing classification line only when the names match exactly. If the names differ, even by punctuation or case, DualEntry auto-creates a new line rather than reusing the existing one.
Troubleshoot sync errors
When a record fails to sync, it appears in the Integration Errors log under Company → Integrations → Paychex Flex. The most common causes:Result
After completing these steps, every Paychex Flex payroll run posts to DualEntry as a single consolidated journal entry, with line items per (pay statement item, department) and a balanced offset entry where needed. To verify the first run, open the consolidated entry for the latest pay date and confirm its memo reads[Paychex Flex] Payroll ..., that total debits equal total credits, and that each earnings, tax, deduction, and contribution line landed in the GL account you mapped. Spot-check a department split against the Paychex payroll report so you know classifications resolved as expected.
To audit the resulting payroll entries, see Journal Entries. For another payroll provider that connects the same way, see the Gusto integration or the Justworks integration. To connect additional systems, return to Integrations.