From the supplier to the warehouse to the pharmacy’s account.
Whether your company is exempt from the invoicing mandate today or required to issue invoices, you record your purchases from suppliers and your credit sales to pharmacies, and you follow your stock across your warehouses.
Accounting software for pharma companies in Jordan starts with each customer’s account: a credit sales invoice, what the customer returned, what they paid and what is left to collect. In a pharmaceutical company in Amman or Irbid you buy from your suppliers and sell to pharmacies and hospitals who pay over weeks, and your items sit in more than one warehouse. In Qoyod, record the purchase invoice under the supplier’s name, then the credit sales invoice for each customer, take what they pay with a receipt voucher, issue a credit note for what comes back, and follow the quantity of each item in each warehouse.
1. Where does a pharmaceutical company’s money scatter?
Before you choose accounting software for a pharmaceutical company in Jordan, look at where your numbers scatter today: each pharmacy’s balance, what came back from it, each rep’s sales, and the quantity in each warehouse.
A customer takes today and pays weeks later
You sell to a pharmacy today and the payments arrive in instalments, so its balance sits in a statement that you keep by hand.
With Qoyod: issue a credit sales invoice, record what the customer pays with a receipt voucher, and follow the balance in the customer statement.
An item comes back after the sale
A pharmacy returns an item, someone edits the invoice by hand, and the stock does not match the balance.
With Qoyod: issue a credit note from the invoice, and a stored item goes back to stock while the customer’s balance goes down.
A rep who sells to dozens of pharmacies
You only see each rep’s sales by adding up the invoices one by one.
With Qoyod: record the rep’s name on the sales invoice in an additional field that you create, and follow their sales in the income statement.
Stock in more than one warehouse
Your items are split between two locations or more, and the purchasing manager does not know what is left in each.
With Qoyod: see the quantity of each item in each warehouse, and set a reorder level so that an alert shows on the dashboard.
2. One cycle: from the supplier’s invoice to the pharmacy’s balance
One cycle, five stops, one new line on the cycle’s numbers card at each.
Stop 1: You buy from the supplier
Record the purchase invoice under the supplier’s name with the quantity and the price per unit, and pay part of it, so the rest stays on the supplier’s balance.
Stop 2: You move part of it to another warehouse
Choose the sending location, the receiving location, the transit account and the quantity, then record the receipt when the goods arrive.
Stop 3: You sell to a pharmacy on credit
Issue a credit sales invoice with the quantity and the price per unit, and the amount shows on the customer’s balance.
Stop 4: The pharmacy returns some items
Create a credit note from the invoice for the quantity returned, so stored items go back to stock and the customer’s balance goes down.
Stop 5: The pharmacy pays part
Record what it paid with a receipt voucher, and follow what remains in the customer statement.
3. Accounting Software for Pharma Companies in Jordan: what Qoyod covers in your company
Electronic invoicing and integrated accounting in one system. And here are six jobs that Qoyod covers in a pharmaceutical company, from the credit sales invoice to the quantity in each warehouse.
A credit sales invoice for each customer
Create a credit sales invoice for each pharmacy or hospital, with your items, their quantities and the price per unit. Each item has the tax setting that you choose when you create it. Qoyod does not support price lists for individual customers, so you write the agreed price on the invoice line.
Each customer’s balance and its collection
Record what a customer pays with a receipt voucher, follow the balance in the customer statement, and compare customer debts across periods in the ageing report. In the sales invoice settings you can turn on an e-mail reminder to the customer to pay, a number of days that you set before the due date, and a weekly e-mail that lists the invoices due from your customers. The reminder goes to the e-mail address in the customer’s details.
Returns by credit note
Issue a credit note from the sales invoice for the items and quantities returned, so a stored item goes back to stock, the customer’s account goes down, and the original invoice stays as it is. Do not use it for a discount on a stored item, because it returns the quantity to stock.
Each rep’s sales
Create an additional field for the rep’s name on sales invoices, and record the name in the “Additional information” tab at the bottom of the invoice. You can then filter the income statement by that name from “Advanced analysis” to see the rep’s sales. Qoyod does not calculate commission, so you work out the rep’s share from their sales yourself.
Warehouses, transfers and the reorder level
Add your warehouses as locations, and see in the product locations report the quantity of each item in each location and the total. Transfer stock between your locations through a transit account, and count each location by its actual quantity so that the difference from the current quantity shows. Set a reorder level for each item in its location, and an alert shows on the dashboard with a “Stock status” chart. The number of locations varies with your subscription, so ask sales what fits your company.
Suppliers and item cost
Record your purchases on purchase invoices under each supplier’s name, and check the balance in the supplier’s statement and in the supplier ageing report. The product cost and margin report shows each item’s average cost and its margin, and you can filter it by location. The cost in it is the average cost.
4. Pharmaceutical companies and the National Invoicing System
Discuss your company’s position with your accountant.
Who must use e-invoicing in Jordan
Whether your company is exempt from the invoicing mandate or required to issue invoices, Qoyod keeps the books for your stock, purchases and cash, and it is integrated with the National Invoicing System (JoFotara) for when you need it.
5. Your accountant shares the decision
If you work with an accountant or an accounting firm, their view on accounting software comes before your decision. The question “is my activity exempt from the invoicing mandate?” belongs with your accountant and the Department. The books belong in Qoyod.
What you see
- Each customer’s balance, what they returned and what they paid.
- Each rep’s sales from the income statement.
- The quantity of each item in each warehouse, and the items that reached the reorder level.
- What each supplier is owed, and what you paid them.
What your accountant reviews
- Purchase invoices, sales invoices and credit notes.
- The journal entries of stock transfers and counts in the journal book report.
- Income statement, balance sheet, trial balance and the ageing of customer and supplier debts.
- Report exports to Excel and PDF.
- If your business must issue invoices: the JoFotara status of each one.
Add your accountant as a user on your account, with the role and permissions you set.
6. Other Qoyod products
Your company’s books run on Qoyod Accounting. For your team there is another Qoyod product: Qoyod HR, on its own subscription.
Qoyod HR
For a pharmaceutical company with a team in more than one branch.
Qoyod HR is available to businesses in Jordan. The connection to Qoyod Accounting is now available.
- Attendance across all your company branches.
- Leave management.
- Payroll with allowances and advances.
7. Frequently asked questions
Does a pharmaceutical company have to issue invoices through the National Invoicing System (JoFotara)?
The e-invoicing mandate covers every seller of goods or provider of services, not only those registered for General Sales Tax, except for activities that the Invoicing Affairs Instructions exempt under set conditions. A seller that is not registered issues an income invoice. Mandatory application has been in force since 1 April 2025, with oversight steadily tightening. Other sectors were added to the list in Article (4) of the Invoicing Affairs Instructions by later amendments, so it is not a closed list. Check the text in force for your activity with the Income and Sales Tax Department.
More detail in our guide to the JoFotara exemption
If a business is not required to issue invoices, does that mean it pays no sales tax?
Not by itself. An exemption from the provisions of the Invoicing Regulation, where one applies, does not on its own exempt anyone from General Sales Tax or income tax, each of which has its own law. Check your tax position with your accountant.
How do I invoice a pharmacy on credit and handle what it returns?
Open Sales, then Invoices, choose New invoice, set the customer and the location you sold from, and choose the payment terms so that Qoyod sets the due date. Then add your items with their quantities, and change the price on a line if you agreed on another, because Qoyod does not support a price list for individual customers. When the customer pays, record a receipt voucher in their name and follow what remains in the customer statement. If the pharmacy returns items, choose Credit notes from the top options of the invoices list, press New credit note, set the customer, the invoice and the reason, and enter the items and quantities returned. The customer’s account goes down, a stored item goes back to stock, and the original invoice stays as it is. Do not use a credit note for a discount on a stored item, because it returns the quantity to stock. And a returned invoice keeps showing in the customer ageing report until you allocate the credit note to it.
Does Qoyod calculate a rep’s commission?
No. Qoyod does not calculate commission. What it offers is recording the rep’s name in an additional field on the sales invoice and following their sales in the income statement, and you work out the agreed share from those sales yourself.
Does Qoyod track the expiry dates and batch numbers of medicines?
No. Qoyod has no tracking of batch numbers or expiry dates. What it offers is each item’s balance and movements in every location, and a periodic stock count that shows slow-moving stock before it expires. The expiry date is read from the packaging.
Does Qoyod deal with the regulatory requirements for medicines and their pricing?
This page shows what Qoyod covers in a pharmaceutical company’s books: invoices, vouchers, balances, warehouse stock with its transfers and counts, and reports. The regulatory requirements for medicines, their pricing and the cold chain are not shown here, so ask the sales team what fits your company.
That brings the company’s numbers together in one place: a supplier you record, a warehouse that knows its quantity, and a customer who knows their balance.
