When employees are on leave, Cocoon helps calculate the leave-related pay amounts employers can use to run payroll. Cocoon generates pay files according to your company’s payroll schedule and Proxy, Workspace and Pay admins will receive an email notification when a pay file is ready to download from the Documents tab in the Cocoon admin dashboard.
Cocoon’s software estimates what employees are owed during leave, including employer-paid leave amounts and estimated state and/or insurance benefit payments. Employers remain responsible for reviewing the file and running payroll through their payroll system.
Understanding the pay file
When you open your pay file, you may see columns highlighted in different colors.
Yellow columns provide the key payroll amounts most employers need to review and use when running payroll.
Blue columns provide supporting details about the employee, leave dates, hours, and payroll calculations.
In most cases, your payroll team should focus on the Total Pay Owed by Employer column. This column summarizes the employer’s pay obligation for the employee for that pay period.
Below are the most important columns to understand.
Employee number
The Employee number is your employee’s unique payroll identifier. This helps ensure the correct pay amounts are applied to the correct employee. This information is typically provided to Cocoon through the employee census or HRIS data your company shares with Cocoon. If an employee does not have a payroll identifies on file, Cocoon may use another employee identifier, such as work email, depending on your company’s configuration.
Full Name
The Full Name column identifies the employee the pay calculation applies to.
Leave type
The Leave Type column identifies the type of leave the employee is taking, such as parental, medical, or caregiver leave.
Leave pay
The Leave Pay column shows the amount of employer leave pay associated with the employee’s leave hours or leave days in the current pay period.
This amount is calculated before any estimated state and/ or insurance benefit payments are applied.
Regular pay
The Regular Pay column shows non-leave pay for the current pay period. Regular Pay is most commonly non-zero when an employee:
starts leave in the middle of a pay period, or
Returns from leave in the middle of a pay period.
For example, if an employee works for part of the pay period and is on leave for the rest, the file may include both Regular Pay and Leave Pay.
Sick Pay and PTO Pay
Cocoon does not generally calculate sick pay or PTO pay as part of the standard leave pay calculation. If these columns appear in your pay file, they are usually included as a separate payroll bucket and may show $0.00 unless your company has a specific configuration or process that uses them.
Benefit Deductions
The Benefit Deductions column shows the estimated state and/or insurance benefit payments Cocoon expects the employee to receive outside of employer payroll.
These amounts reduce the employer’s pay obligation for the pay period. Because they reduce what the employer news to pay directly, they typically appear as negative values in the pay file.
For example, if an employee is expected to receive $1,000 from a state paid leave program, Cocoon may show -$1,000 in the Benefit Deductions column. This does not mean Cocoon is deducting from the employee’s earned wages. Instead, it means Cocoon is accounting for benefits the employee is expected to receive from another source.
Cocoon estimates these benefits based on the employee’s leave plan, location, leave type, applicable state or insurance programs, and information available in Cocoon at the time the pay file is generated.
Total pay owed by employer
The Total Pay Owed by Employer column shows the total amount your company owes the employee for the pay period based on Cocoon’s calculation.
In the standard pay file, this is generally calculated as:
Leave Pay + Regular Pay + Sick Pay + PTO Pay - Estimated Benefit Deductions = Total Pay Owed by Employer
This is the main column your payroll team should use to determine the amount the employer should pay the employee for the pay period.
Additional calculations details
If you scroll to the right in the pay file, you may see additional columns with supporting details. These can include items like leave dates, pay period dates, hours, workdays, salary, hourly rate, or other values used in the calculation.
These columns are primarily informational. They can help your team understand how Cocoon calculated the payroll amounts, but they are not usually required to run payroll.
What happens if leave information changes after a pay file is published?
If an employee’s leave details change after Cocoon has published a pay file, the update may be reflected in a future pay cycle.
Depending on the type of change, Cocoon may provide:
An adjustment file, or
An updated calculation in a future payroll file.
Adjustment files are generally used to show changes in how pay should be categorized across prior pay periods, such as updates between Paid Leave, Unpaid Leave, and Regular Pay.
For example:
If a leave date change means the employee should have been paid for an unpaid day, the adjustment file may show a positive amount.
If a leave date change means the employee was paid for a day that should have been unpaid, the adjustment file may show a negative amount.
If pay is simply reclassified between Regular Pay and Leave Pay with no change in total pay, the adjustment file may show a $0 impact.
Changes to estimated benefit amounts may be reflected in future payroll calculations rather than as a separate adjustment-file line item.
If your company processes payroll using amounts that differ from Cocoon’s finalized pay file, those differences generally need to be reconciled outside of Cocoon. Cocoon can help explain how the original calculation was produced, but finalized payroll files may not be retroactively updated to match downstream payroll changes.
Example Scenarios
Scenario 1: Employee starts leave in the middle of a pay period
Alvin is taking a medical leave through Cocoon. During this pay period, Alvin worked for part of the pay period and then started leave.
Because Alvin worked before starting leave, the pay file includes both Regular Pay and Leave Pay.
Example:
Leave Pay: $3,365.50
Regular Pay: $2,884.50
Benefit Deductions: -$3,750.00
The Leave Pay amount reflects the employer leave pay associated with Alvin’s leave time during the pay period, before estimated benefits are applied.
The Regular Pay amount reflects the non-leave time Alvin worked before starting leave.
The Benefit Deductions amount reflects estimated state and/or insurance benefits Alvin is expected to receive outside of employer payroll. Because those benefits reduce the employer’s pay obligation, they appear as a negative value.
The Total Pay Owed by Employer combines these amounts:
$3,365.50 + $2,884.50 - $3,750.00 = $2,500.00
In this example, the employer would pay Alvin $2,500.00 through payroll for the pay period.
Scenario 2: Employee starts leave at the beginning of a pay period
Mariana is taking parental leave, and the leave starts on the first day of the company’s pay period.
Because Mariana did not work during the pay period, the pay file shows $0.00 in Regular Pay.
Example:
Leave Pay: $8,333.33
Regular Pay: $0.00
Benefit Deductions: -$4,166.67
The Leave Pay amount reflects the employer leave pay associated with Mariana’s leave time before estimated benefits are applied.
The Benefit Deductions amount reflects estimated benefits Mariana is expected to receive from state and/or insurance programs. Because those benefits reduce the employer’s pay obligation, they appear as a negative value.
The Total Pay Owed by Employer combines these amounts:
$8,333.33 + $0.00 - $4,166.67 = $4,166.66
In this example, the employer would pay Mariana $4,166.66 through payroll for the pay period.
Scenario 3: Employee is not eligible for state or insurance benefits
Ning is taking parental leave starting on the first day of the company’s pay period. Based on Ning’s location, leave type, and available benefit programs, Cocoon does not estimate any state or insurance benefits for this leave.
Example:
Leave Pay: $8,333.33
Regular Pay: $0.00
Benefit Deductions: $0.00
Because there are no estimated state or insurance benefits, the Benefit Deductions column is $0.00.
The Total Pay Owed by Employer combines these amounts:
$8,333.33 + $0.00 - $0.00 = $8,333.33
In this example, the employer would pay Ning $8,333.33 through payroll for the pay period.
Best practices for payroll teams
To help ensure employees are paid accurately while on leave:
Download and review each Cocoon pay file when it becomes available.
Confirm the employee identifier and employee name match your payroll system.
Review the Total Pay Owed by Employer column for each employee.
Use the supporting columns as needed to understand leave dates, hours, and calculation details.
Review any adjustment files provided in future pay cycles.
Contact Cocoon Support if you have questions about how a specific amount was calculated.
Cocoon’s pay files are designed to give payroll teams a clear starting point for processing leave-related payroll while accounting for estimated state and/or insurance benefit payments.
Questions? Please reach out to the Support team at: