How to Connect Your ATS to Payroll and Onboarding in Five Steps
Connecting an applicant tracking system (ATS) to payroll and onboarding takes five steps, each tied to an event or deadline. The accepted offer starts the handoff. The employee supplies Form W-4 and Section 1 of Form I-9, and the employer completes Section 2. Any background check follows its own track. Payroll is set up before the first wage payment, and the state receives the new-hire report within 20 days of hire at the latest.
Four federal dates set the schedule for new-hire data
These four federal dates apply when you hire an employee, as of October 2026.
Milestone
What is due
Source
First day of employment
The employee completes Section 1 of Form I-9, the employment eligibility verification form, no earlier than offer acceptance.
USCIS, Handbook for Employers M-274, section 2.0
Three business days after the first day
The employer completes Section 2. A Monday start gives a Thursday deadline, and a job lasting fewer than three business days makes Section 2 due at the time of hire.
USCIS, M-274 section 2.0
First wage payment
The employee’s signed Form W-4, the federal withholding certificate, takes effect.
IRS, Publication 15 (2026)
Within 20 days of hire
The federal outer limit for reporting the new hire to the state. Some states require it sooner.
HHS, New Hire Reporting
Per IRS, Publication 15 (2026), a new employee who gives no Form W-4 is treated as Single or Married filing separately (Step 1(c)) with no other entries.
The date of hire is the date the employee first performs services for pay, which can be earlier than the start date on the offer if paid work begins sooner (HHS, New Hire Reporting).
First, start the handoff when the candidate accepts the offer
The HR lead, office manager, or hiring manager runs this step when a candidate accepts a written offer.
What you need first. The written offer, the applicant record in your ATS, and the exempt or non-exempt classification decision.
1. List the fields the accepted offer carries (title, pay rate or salary, pay basis, classification, start date, and work state).
2. Set the classification before pay. Job title alone does not establish exempt status, because salary and duties both matter (DOL, 29 CFR 541.2). The executive, administrative, and professional exemptions generally require a salary of at least $684 per week as of October 2026 (DOL, 29 CFR 541.600), and states may set their own rules, so check your state labor agency.
3. Start the Form I-9 Section 1 request through onboarding after the candidate accepts, and keep it out of the application. An employer may not ask a person who has not accepted the offer to complete Section 1 (USCIS, M-274 section 3.0).
4. Ask each vendor in writing which fields cross at offer acceptance, which stay manual, and who completes them. Ask whether the trigger is the accepted offer or a scheduled batch, and which mechanism carries each field (a connection built into one vendor’s platform, an API link between separate systems, or a file export).
5. Employers covered by federal anti-discrimination law must keep application forms and other hiring records at least one year from the record or the hiring decision, whichever is later (EEOC, 29 CFR 1602.14). Ask the vendor in writing how applicant records are retained and exported.
What a correct result looks like. A written list of the offer fields, the system that holds each, and the vendor’s written answer on which fields cross at acceptance and which stay manual.
Asure Recruiting provides offer management with e-signature and connects directly into AsureCentral, so a hired candidate flows into onboarding without re-entry. On AsureCentral, payroll, HR, tax, benefits, recruiting, time and attendance, and employee self-service connect on one platform with one login.
Second, capture what the employee supplies and what the employer completes
The HR lead or payroll administrator runs this step as onboarding forms come in.
What you need first. The current Form I-9 edition, a Form W-4, your state’s withholding form, and the employee’s direct deposit details.
1. Complete Section 2 yourself or through an authorized representative after examining original, unexpired documents or an acceptable receipt, and let the employee choose which acceptable documents to present (USCIS, M-274 section 2.0 and USCIS, M-274 section 4.0).
2. Ask the employee for a signed Form W-4 when work starts, keep it on file, and show the original to the IRS on request (IRS, Publication 15 (2026)). Withholding follows a valid signed form unless the IRS directs otherwise by notice. State withholding forms vary by state, so check your state agency.
3. Ask each vendor in writing whether its electronic Form I-9 system meets the electronic-system standards in DHS, 8 CFR 274a.2(e) to (i) and uses the current edition, dated 01/20/25 as of October 2026 (USCIS, Form I-9).
4. Ask each vendor in writing whether its electronic Form W-4 meets the electronic submission requirements in IRS, Publication 15-T (2026).
5. Keep Form I-9 content on its own track. By statute, the form and information on or appended to it may not be used for purposes other than enforcement of the immigration chapter and four sections of title 18 (GPO, 8 U.S.C. 1324a(b)(5)). Ask each vendor in writing whether I-9 content stays out of payroll fields, and check with employment counsel before mapping any I-9 field into a payroll record.
What a correct result looks like. Section 2 completed by a named person from the original documents the employee chose, a signed Form W-4 on file, and written vendor answers on electronic form standards and I-9 content.
Third, run any background-check authorization on its own track
This step applies only if you run a check through a screening company under the Fair Credit Reporting Act (FCRA). It runs separately from the I-9 and W-4 steps, and in this sequence it follows a written conditional offer.
What you need first. A written conditional offer, a stand-alone disclosure document, and an account with a screening company.
1. Send a written conditional offer before any conviction-history inquiry. California (five or more employees) and New York City (four or more employees) generally require the conditional offer to come first, and other places vary, so check your state agency (California Civil Rights Department and NYC Commission on Human Rights).
2. Give the written disclosure as a document that consists solely of the disclosure, and get written authorization before the report is procured. The authorization may be on that document, and the notice cannot sit inside an employment application (FTC, Background Checks guidance and Legal Information Institute, 15 U.S.C. 1681b).
3. Certify to the screening company that you gave notice, got permission, and complied with the FCRA (FTC, Background Checks guidance).
4. Before any adverse action based in whole or in part on the report, give the person a copy of the report and the summary of rights (FTC, Background Checks guidance). The statute and the FTC guidance do not set a waiting period, and the FTC says the notice lets the person review the report and explain negative information. If the decision rests on conviction history, California and New York City also require at least five business days to respond (California Civil Rights Department; NYC Commission on Human Rights).
5. After adverse action, notify the person of the action, the screening company’s name, address, and phone number, that the company did not make the decision, and the right to dispute accuracy and get a free additional report within 60 days (FTC, Using Consumer Reports).
6. Ask each ATS and onboarding vendor in writing whether the disclosure stays a separate document and stays out of the application.
What a correct result looks like. A signed stand-alone authorization on file before the report is ordered.
Fourth, set up payroll before the first wage payment
The payroll administrator or HR generalist runs this step before the first wage payment.
What you need first. The signed Form W-4, the direct deposit form, the accepted offer record, and your state labor agency’s payday rules.
1. Enter withholding from the signed Form W-4 using the IRS withholding methods in IRS, Publication 15-T (2026) or an automated system built on them.
2. Enter direct deposit account and routing numbers exactly as the employee submitted them. Direct deposit is an acceptable payment method if the employee may choose cash or check (DOL, Field Operations Handbook, chapter 30). Check your state labor agency for direct deposit rules.
3. Confirm pay rate or salary, pay basis, and classification against the offer, and set the date of hire to the date the employee first performs services for pay. Wages under the Fair Labor Standards Act are due on the regular payday for the pay period covered (DOL, Handy Reference Guide), and payday rules vary by state (DOL, State Payday Requirements), so check your state labor agency.
4. As a recommended practice, set a payroll cutoff for onboarding data ahead of the first pay run and name who completes anything still missing, because the dates above apply whatever other onboarding tasks remain.
5. As a recommended practice, check the payroll record against the offer, the signed Form W-4, and the direct deposit form before the first run.
6. Ask each vendor in writing who is alerted when a transfer fails, whether test records can be kept out of live payroll, deposits, W-2s, and state reports, and how all data can be exported if you leave.
What a correct result looks like. A payroll record that matches the offer and the signed forms before the first wage payment, with a named person responsible for each field still entered by hand.
Fifth, report the new hire to the state by its deadline, no later than 20 days after hire
The payroll administrator runs this step for each new employee.
What you need first. The seven data elements from the payroll record and the state agency that receives reports for the state where the employee works.
1. Pull the seven required elements from the payroll record (employee name, address, and Social Security number, date of hire, and employer name, address, and federal employer identification number, or FEIN) (HHS, New Hire Reporting).
2. Send the report to the designated state agency for the state where the employee works. It goes to the state, not to the IRS.
3. Treat a person rehired after 60 or more consecutive days of separation as a new hire (IRS, Publication 15 (2026) and HHS, New Hire Reporting).
4. Check your state agency, because some states require the report sooner or require data elements beyond the seven federal ones (HHS, New Hire Reporting).
5. Ask each vendor in writing whether the system submits the state report, for which states, and with what extra data. Name the person who submits it if the vendor does not. The reporting duty stays with the employer.
What a correct result looks like. A state report submitted by a named person, or by a vendor that has said in writing it submits the report, with the seven elements matching the payroll record.
Frequently asked questions
When can the Form I-9 go out to a new hire?
Section 1 of Form I-9 can go out after the candidate accepts the offer, and the employee completes it by the first day of employment. Before acceptance, an employer may not ask for Section 1 (USCIS, M-274 section 3.0).
Which new-hire data comes from the offer, and which comes from the employee?
The accepted offer carries the title, pay rate or salary, pay basis, classification, start date, and work state. The employee supplies the signed Form W-4, Section 1 of Form I-9, the choice of acceptable documents, and direct deposit details. The employer completes Section 2 of Form I-9 and the state new-hire report (IRS, Publication 15 (2026); USCIS, M-274 section 4.0).
What must an electronic Form W-4 do?
Receiving Form W-4 electronically is optional, and the system must ensure the data received is the data sent, log each access that results in a submission, make it reasonably certain the submitter is the employee, match the paper form, take the e-signature last under the form’s perjury language, produce a hard copy for the IRS on request, and meet paper recordkeeping rules (IRS, Publication 15-T (2026)).
When is the state new-hire report due?
The state new-hire report is due within 20 days of hire to the state where the employee works, and some states require it sooner. A multistate employer may report each hire to the state where the person works or register with HHS and report all hires to one chosen state (HHS, New Hire Reporting).
Can the background-check authorization be part of the onboarding packet?
The disclosure has to be a stand-alone document, and the written authorization may be on that document. The FTC says the notice cannot sit inside an employment application, so keep it out of any application form in the packet (FTC, Background Checks guidance).
Talk to an expert at Asure
AsureCentral lets you run payroll and HR yourself. AsureWorks is a managed service and a PEO alternative with no co-employment. Asure specialists handle day-to-day HR administration, including new hires and changes, on AsureCentral, and you remain the employer of record. Your legal responsibilities as an employer stay with you. The Payroll & HR page describes one platform, two ways to work. Talk to an Asure expert about AsureCentral or AsureWorks.
