How to Do QuickBooks Payroll: Step by Step Handling of Payroll in QuickBooks

Handling payroll can be an incredibly complex and time-consuming process for any business.

Luckily, QuickBooks offers a user-friendly payroll system that can automate and streamline the entire payroll process so you can focus on running your business.

In this post, we'll walk through the key steps for setting up payroll in QuickBooks, processing payroll from start to finish, handling taxes, leveraging direct deposit, using the QuickBooks Payroll mobile app, and taking advantage of additional helpful features.

Introduction to QuickBooks Payroll Handling

Handling payroll can be a complex and time-consuming task for many businesses. QuickBooks Payroll provides a streamlined solution to manage payroll right within your QuickBooks account. This allows you to automate payroll tasks, calculate taxes accurately, pay employees quickly, and eliminate the need to outsource payroll.

In this article, we will walk through the key aspects of using QuickBooks Payroll:

Understanding QuickBooks Payroll Service

QuickBooks Payroll is an add-on service that seamlessly integrates with QuickBooks Desktop or QuickBooks Online. It handles all the calculations for payroll taxes, deductions, withholdings, and more based on latest tax rates and regulations. You can process payroll, print checks, pay payroll taxes, generate forms, and access reporting right within QuickBooks.

Some of the main features include:

Automatic federal, state, and local payroll tax calculations
Direct deposit for employee payroll
Integration with bank accounts to pay payroll taxes
W-2 and 1099 tax form preparation
Various payroll reports on compensation, taxes, deductions etc.

Advantages of In-House Payroll with QuickBooks

Handling payroll in-house using QuickBooks Payroll provides several benefits:

Cost Savings: No need to pay for an external payroll service provider. Just a low monthly fee per employee.
**Accuracy:**Automated tax calculations prevent errors and penalties.
Convenience: Process payroll tasks efficiently without leaving QuickBooks.
Control: Get real-time insight into payroll costs to make better decisions.
Compliance: Automatically updated based on changing regulations.

With QuickBooks streamlining payroll processes, you can focus on your business while saving time and money on paying employees accurately and on time.

How do you process payroll in QuickBooks?

QuickBooks Desktop Payroll allows businesses to easily handle payroll tasks. Here are the key steps to process payroll:

Select Employees, then Pay Employees, and choose from check types like Scheduled Payroll, Unscheduled Payroll or Termination Check.
Select the appropriate payroll schedule, and click Start Scheduled Payroll.
Verify the Pay Period Ends date, Check Date, and the QuickBooks bank account to withdraw funds from.
Review employee payroll details like pay rates, hours worked, deductions etc. Make any corrections if needed.
Click Calculate Payroll for QuickBooks to calculate taxes, deductions, net pay etc.
Review all payroll totals and amounts. Make final corrections if required.
Click Pay Employees to finalize payroll. Print or send pay stubs to employees.

Following these steps allows you to accurately process payroll on time while keeping proper records. Reach out to Intuit support if you need help with more advanced QuickBooks Payroll features.

What are the steps in the payroll process?

Here is a summary of the key steps involved in processing payroll in QuickBooks:

Choose a payroll system

The first step is deciding whether to use QuickBooks Desktop or QuickBooks Online for your payroll needs. QuickBooks Online Payroll offers a simpler setup and is ideal for smaller businesses, while QuickBooks Desktop Payroll provides more advanced payroll features for larger companies.

Create a payroll policy

You'll need to define your company's payroll policies related to pay cycles, pay dates, overtime rules, expense reimbursements, and more. Your accountant can help establish compliant payroll guidelines aligned with labor laws and tax requirements.

Gather employee information

To set up payroll for each employee, collect details like salary information, mailing address, bank account, tax forms, and deductions to enter into QuickBooks payroll. Setting up direct deposit ensures convenient paycheck delivery.

Establish a time-tracking system

Implement a system for tracking employee work hours such as time clocks or timesheet software integrated with QuickBooks. Accurate hour logs are essential for proper wage and overtime calculations.

Collect employee timesheets

Make sure employees submit electronic or paper timesheets each pay period for manager review and approval before payroll is processed.

Approve and submit payroll

Review all employee hours for accuracy. Then approve and process payroll in QuickBooks based on your pay cycle schedule. Print or download reports to review before paychecks are delivered via direct deposit.

Report and update payroll records

Run monthly, quarterly and annual payroll tax reports in QuickBooks to submit returns and payments to tax agencies. Also update payroll records for new hires, terminations, raises or deduction changes.

This summarizes the key steps for handling payroll processing efficiently within QuickBooks while remaining compliant with IRS regulations. Let me know if you need any clarification or have additional questions!

How do you manually process payroll?

Manually processing payroll can be tedious but necessary for many small businesses. Here are the key steps to handle payroll yourself:

Calculate gross wages based on hours worked, salary agreements, commissions earned, etc. for each employee. Track all income that must be included in gross wages.

Determine payroll deductions like federal, state, and local taxes; Social Security and Medicare contributions; 401(k) contributions; health insurance premiums; etc. based on each employee's W-4, benefits selection, and relevant payroll laws.

Withhold deductions from gross wages to determine net pay for each employee. Withholdings must be paid to the appropriate agencies even if doing payroll manually.

Pay employees their net wages. Print/provide pay stubs detailing their gross wages, deductions, net pay, and relevant YTD totals. Consider direct deposit or pay cards to eliminate paper checks.

Pay tax authorities all company and employee payroll taxes that were withheld. File associated tax forms detailing wages paid and taxes owed.

Maintain payroll records like pay stubs, W2s, tax payments, employment records, etc. Keep records safe for reference. Retain records based on regulatory requirements.

The key to doing DIY payroll manually is closely following all state, federal, and local payroll compliance rules to avoid penalties down the road. Consider payroll software if volume becomes difficult to handle manually. Let us know if you need help!

How do I run manual payroll in QuickBooks?

To set up manual payroll in QuickBooks Desktop, follow these steps:

From the Edit dropdown menu, select Preferences.
Select Payroll & Employees, then select the Company Preferences tab.
In the QuickBooks Desktop Payroll Features section, select the Full payroll and the Manual Payroll checkboxes. This will enable full payroll functionality and manual payroll entry in QuickBooks.
Click OK to save the changes.

With manual payroll enabled, you can enter payroll information for employees directly without integrating with online payroll. This allows you to have more control and flexibility over payroll, though you will need to handle payroll tax payments and filings yourself.

Some key things to keep in mind when running manual payroll:

Calculate payroll taxes and deductions accurately for each pay period
Remit payroll taxes on time to avoid penalties
File required payroll tax forms
Issue W-2s at year-end

So in summary, enabling manual payroll in QuickBooks Desktop gives you more control over payroll processing while requiring you to handle additional responsibilities compared to integrated online payroll services.

Initial Setup for Payroll in QuickBooks Online

Activating QuickBooks Payroll Service

To activate QuickBooks Payroll, first log into your QuickBooks Online account. Under the Employees menu, select "Get started with payroll". You will then need to select the appropriate QuickBooks Payroll plan based on the number of employees you need to pay. QuickBooks offers a Core, Premium, and Elite payroll plan. Follow the prompts to sign up for the level of service you need.

If using QuickBooks Desktop, open the Employees menu and click "Turn on Payroll". Follow the activation prompts from there.

Inputting Company Payroll Information

Once QuickBooks Payroll is activated, you will need to input your company's payroll details. This includes your business address, federal and state tax IDs, bank account for payroll transfers, unemployment insurance details, and workers' compensation insurance details if applicable.

Accurately entering all company payroll details ensures your taxes and regulatory forms are filled properly.

Registering Employee Details in QuickBooks

To pay employees, you first need to register them as employees within QuickBooks. Under the Employees menu, select "Add an employee".

For each employee, you will need to enter details like their name, date of birth, address, salary/pay rate, federal tax withholdings, and any voluntary deductions.

Inputting correct employee details enables accurate payroll calculations and proper tax payments on their behalf.

Configuring QuickBooks Payroll Settings

Within QuickBooks Payroll, you can configure settings like pay schedules, vacation and sick time tracking, reimbursements, garnishments if needed, and more.

Evaluate your preferences and policies to determine the optimal configuration for payroll calculations, direct deposits, and paystub generation in QuickBooks.

Managing Payroll Transactions

Scheduling Payroll Runs in QuickBooks

You can set up payroll schedules in QuickBooks to automatically process payroll on a recurring basis. Here are the steps:

Go to Employees > Payroll Schedules. Click "New Payroll Schedule".
Enter a name and select the employees to pay on this schedule.
Choose the pay period, first pay day, and frequency of pay days. For example, weekly, bi-weekly, semi-monthly etc.
Click OK. QuickBooks will now automatically add payroll transactions for the selected employees using this schedule.

Calculating Pay and Deductions Automatically

QuickBooks payroll feature automatically calculates gross and net pay for employees based on:

Hourly wage or annual salary
Hours worked per pay period
Federal, state, and local tax deductions
Other deductions like medical insurance premiums

As an admin, you just need to enter basic details like pay rates, deductions, and hours. QuickBooks handles all the payroll calculations behind the scenes.

Issuing Direct Deposits and Checks

To pay employees, you can:

Print paychecks directly from QuickBooks.
Use Direct Deposit and deliver wages electronically to bank accounts.
Issue pay cards that allow employees to withdraw funds.

Direct Deposit is fast, secure and convenient for employees. To set it up go to Employees > Payroll Settings > Direct Deposit.

To process payroll, login to your QuickBooks Payroll account online and:

Review employee hours and make any necessary adjustments.
Submit payroll for processing.
Verify if any actions are needed on your part.
Confirm the net pay and deductions are accurate.
Issue payments with one click.

Logging in regularly allows you to manage payroll seamlessly.

Handling Payroll Taxes within QuickBooks

QuickBooks offers robust capabilities to automate payroll tax calculations, payments, and filings. This enables businesses to efficiently handle this critical but complex requirement.

Automating Payroll Tax Calculations

QuickBooks Payroll seamlessly tracks tax liabilities over time based on payroll runs. It automatically calculates federal and state income tax withholdings, Social Security, Medicare, federal and state unemployment taxes. This removes the manual calculation burden.

Preparing Year-End Tax Documents

At year-end, QuickBooks Payroll can generate and deliver critical tax documents like W-2s and 1099 forms to employees and contractors. This simplifies year-end tax reporting.

E-Filing Taxes with QuickBooks

QuickBooks enables e-filing payroll forms and tax payments directly to the IRS and state agencies. This eliminates paper-based submissions. e-filing also reduces errors and speeds up processing.

Does QuickBooks Do Payroll Taxes for You?

While QuickBooks automates tax calculations and payments, businesses are still responsible for ensuring tax payments are made on time. QuickBooks does not automatically withdraw or submit payroll taxes without user input. So oversight is still required.

In summary, QuickBooks Payroll provides sophisticated yet easy-to-use tax management capabilities. This makes handling payroll taxes much less complex for most businesses. Critical capabilities like calculations, payments, reporting and compliance filings are automated. But oversight is still needed to validate figures and approve submissions.

Direct Deposit Management in QuickBooks

Managing payroll can be a complex process, especially when it comes to paying employees. Direct deposit can help streamline payments and provides a secure method for compensating staff. QuickBooks offers direct deposit capabilities to ease the payroll process.

Setting Up Direct Deposit in QuickBooks Online

Setting up direct deposit in QuickBooks Online is straightforward. Simply navigate to the Payroll settings and click "Direct Deposit." You can then enter bank account information for each employee. QuickBooks will store this data to process payments each pay period.

Be sure to confirm the account and routing numbers for each employee's bank account. Check that funds arrive as expected after the first payroll run with direct deposit activated. Notify employees of when deposits will be available based on your pay schedule.

Understanding QuickBooks Direct Deposit Cost

Using direct deposit with QuickBooks does come at a small additional cost. You will need to subscribe to the QuickBooks Payroll service, which starts at $45 per month. An extra $4 fee is charged per employee receiving funds through direct deposit each month.

While this represents some overhead, streamlining payroll through direct deposit can create significant time savings and reduce the chance of errors. For most small businesses, the efficiency gains are well worth the monthly subscription and transaction costs.

Ensuring Secure Payroll Transactions

Security is crucial when dealing with sensitive information like bank accounts and payroll data. QuickBooks leverages bank-level encryption and security protocols to protect direct deposit transactions. Access to payroll features requires strong user permissions, and the QuickBooks security dashboard enables monitoring for suspicious activity.

Before choosing direct deposit, ensure your accounting system and company network are properly secured against potential threats. Turn on two-factor authentication for an additional layer of login protection. With strong security measures in place, direct deposit can safely ease the payroll burden.

Leveraging the QuickBooks Payroll App

The QuickBooks Payroll app provides a convenient way to manage payroll tasks on the go directly from your mobile device. With full integration across QuickBooks Desktop, QuickBooks Online, and the QuickBooks Payroll app, you can easily access and manage payroll data no matter where you are.

Mobile Payroll Management

The QuickBooks Payroll mobile app makes it easy to handle payroll tasks on the go. Instead of being tied to your computer, you can review payroll summaries, approve timesheets, and make any necessary changes directly from your phone or tablet. This gives you flexibility to run payroll from anywhere.

For example, if you need to approve an employee's timesheet request while out of the office, the QuickBooks Payroll app lets you quickly handle this essential payroll task remotely. The app also provides an overview of upcoming payroll deadlines so you can stay on top of what needs to be done. With mobile access, you don't need to worry about getting behind just because you're away from your desktop.

App Features and Functionality

Key features of the QuickBooks Payroll mobile app include:

Timesheet approvals - Review and approve timesheets right from the app
Payroll summaries - See at-a-glance overviews of upcoming payroll runs
Direct deposit setup - Enter employee direct deposit information
Tax form management - Access payroll summaries and tax documents
Notifications - Receive mobile alerts about approaching deadlines
Employee access - Let employees view their payroll info from their devices

The app seamlessly syncs all data with QuickBooks Desktop and QuickBooks Online Payroll. Any changes made on one platform automatically update across the others.

QuickBooks Payroll App Security

Intuit prioritizes security for all of its mobile apps. The QuickBooks Payroll app leverages encryption, password protection, multi-factor authentication, and other measures to keep your data safe.

Only authorized users can access payroll information through the app. Strong password requirements prevent unauthorized logins. All connections use bank-level encryption protocols to protect sensitive data like employee SSNs, bank account details, etc.

With rigorous security enforced natively at both the software and hardware levels, you can use the QuickBooks Payroll app to manage payroll tasks remotely with peace of mind.

Additional QuickBooks Payroll Features and Tools

QuickBooks Payroll provides a robust set of features beyond basic payroll processing to help businesses streamline operations.

Accessing Detailed Payroll Reports

QuickBooks Payroll offers built-in reporting to help businesses analyze payroll costs and liabilities over time. Key reports include:

Payroll Summary - Summary of total pay, deductions, taxes, etc. for a pay period
Payroll Item Detail - Breakdown of each payroll item per employee
Payroll Liabilities - Summary of outstanding tax liabilities
Payroll Transactions - List of all payroll transactions

These reports enable deeper visibility into payroll expenses to inform budgeting and cost management.

Empowering Employees with Self-Service

The QuickBooks Payroll self-service portal allows employees to access pay stubs, set up direct deposit, update personal information and more. This saves HR teams time on administrative tasks while giving employees transparency and control.

Key self-service capabilities include:

Access digital pay stubs
Change direct deposit information
Update personal info like address and tax forms
View leave balances and time-off requests
Download tax documents like W-2s

Enabling employee self-service frees up HR staff to focus on more strategic initiatives.

Integrating Payroll with Other Business Functions

QuickBooks Payroll integrates with other Intuit products like QuickBooks Accounting and QuickBooks Time to connect payroll with the general ledger, billing, and time tracking.

It also offers integration with many third-party apps for:

Human resource information systems (HRIS)
Benefits administration
Applicant tracking systems (ATS)
Time and attendance

These integrations allow data to flow automatically between systems, reducing double entry and manual errors.

Customizing Payroll to Support Business Needs

QuickBooks Payroll is highly customizable to meet the needs of different business models and workforce structures:

Payment schedules - Weekly, biweekly, semi-monthly, monthly
Pay types - Hourly, salary, per project, commissions, etc.
Deductions and reimbursements - Customized earning and deduction types
Tax setups - Supports multiple state and local tax rates
Overtime calculations - Applicable overtime rules and calculations

This flexibility enables QuickBooks Payroll to scale as business and payroll complexity increases over time.

Conclusion: Streamlining Your Payroll with QuickBooks

Handling payroll can be a complex process, but QuickBooks simplifies it with automation and easy-to-use tools. By following the key steps covered in this guide, you can seamlessly manage payroll end-to-end directly within QuickBooks.

The major benefits of handling payroll in QuickBooks include:

Automatic tax calculations and payments: QuickBooks accurately calculates payroll taxes and can even submit them on your behalf, saving you time on tax compliance.
Built-in direct deposit: Set up direct deposit easily without extra fees, ensuring your employees get paid quickly and securely.
Real-time payroll tracking: Always know your payroll costs and keep your books up to date in real time as you run payroll in QuickBooks.
Simple payroll setup: QuickBooks payroll is intuitive to configure for your small business with helpful wizards guiding you. You can be up and running with payroll fast.

By following this comprehensive guide on setting up payroll yourself or working with a bookkeeper to streamline the process, QuickBooks makes handling payroll efficient so you can focus on operating your business.