How to do a stock count in your medical store without closing the shop
You do not need to pull the shutter down for a day to count stock. Plan the count rack by rack, count in tablets, keep billing safely while you count, then post the differences and chase the shortages with a clear trail.
Many owners put off counting because they think it means closing for a day and losing sales. It does not. A pharmacy stock count can be done one rack at a time, in quiet hours, while the counter keeps billing, as long as you follow a few rules about what to count first and when to sell.
Why count at all
Records drift, even in a careful shop. A bottle breaks and nobody records it. A strip goes to a relative without a bill. A delivery is shelved but its bill is never entered. A cashier bills a strip when the customer took a whole box. Each slip makes your reorder list, your expiry list and your profit a little wrong. A count puts them right, and shows you where the leaks are.
Plan the count
Split the shop into sections
List every place stock lives: each rack, the fridge, the counter drawers, the godown or store room. Treat each one as its own small count. A rack finished in an hour is better than a whole-shop count that drags on for three days.
Pick quiet hours
Before opening, a Sunday morning, after the shutter comes down, or the slow hour after lunch. Never during the evening rush.
Count in base units
Count tablets, capsules, sachets and bottles, not "2 boxes and 3 strips". Pack sizes differ from product to product, and loose strips and single tablets are where mistakes hide. Two full boxes of 10 strips × 10 capsules, plus 3 loose strips, is 230 capsules. A sealed box can be counted as full. An opened one is counted strip by strip.
Controlled drugs first
Count narcotic, psychotropic and other controlled medicines first, while you are fresh, with two people present. Check the result against your register the same day. For what that register must contain and how often it must be checked, ask the regulator.
Bring the records up to date
Before you start, enter every delivery bill for stock already on the shelf, and any return you have already handed to the distributor. Record the breakage you know about, and write off the expired stock you are about to throw away. Otherwise these show up as count differences and hide the ones you really need to find.
Two people per section
One reads out the product, batch number, expiry and quantity. The other writes or types. If you can, avoid having someone count the only rack they look after.
Keep selling during the count
The key idea: a count compares what you find with what the records said at the moment the count started. Anything that moves stock after that moment, on a shelf you have not counted yet, looks like a difference.
Say the records show 120 tablets of a batch when the count starts. If you count that shelf and then sell a strip, all is well. If you sell a strip first and then count 110, the count shows a shortage of 10 on top of the sale.
So:
- Start each section's count just before you count it, not first thing in the morning for the whole shop.
- Count a shelf before you sell from it. If a customer needs something from an uncounted shelf, count that item first. It takes a minute.
- Once a shelf is counted, sell from it freely.
- Keep a new delivery in its carton until its section is counted, and treat a customer return the same way.
- Bill every sale, cash or udhaar. A sale noted down "to bill later" turns into a shortage.
Post the differences and find the cause
Recount before you post
Recount any large difference. A whole box missing is more often a miscount, or a box sitting on another rack, than a real loss.
Read the pattern before you blame anyone
| What you see | Likely cause | What to do |
|---|---|---|
| One batch short, another batch of the same product over by the same amount | Staff took packs from the wrong batch | Fix the shelf order. No stock was lost. |
| Short by exactly a strip or a box | Billed in the wrong unit, or pack size set up wrong | Check the product's units and recent bills |
| Stock on the shelf that is not in the records | A delivery bill not entered, or opening stock missed | Enter the bill. If there is none, add it as found stock. |
| Small shortages across many products | Breakage not recorded, strips given without a bill | Tighten the daily recording habit |
| Repeated shortages of the same costly or controlled items | Possible theft | Watch closely and limit who handles them |
Write down what you found next to the count's reference number, so next time you know where to look.
How often to count
| What | How often |
|---|---|
| Controlled drugs | Weekly, or as the rules require |
| Fast movers and costly items | Monthly |
| One rack or section, in rotation | Every week |
| The whole shop | At least once a year, before your year-end accounts |
| After something unusual, such as a staff member leaving, a break-in or a leak in the store room | Straight away |
Cycle counts
A cycle count is a small count of one part of the shop, done on a schedule so that every rack gets counted in turn. Make a rotation list and count one or two sections a week. Nobody has to close, differences are caught while people still remember what happened, and the year-end count becomes a check rather than a crisis.
How MediPOS records the count
Paper sheets work, but someone has to type the result in later, and the reasons get lost. In MediPOS the count itself is the record.
Go to Inventory → Stock counts and start a count. Give it a name such as Rack A antibiotics, choose the location (Main Store or Quarantine) and, if you like, narrow it with Only products matching, for example syrup. MediPOS lists every batch with stock there, with the system quantity at that moment. That is the snapshot every difference is measured against.
The count sheet shows each product, batch and expiry, with the system quantity and a box for what you counted, both in base units. Under each product name you also see the stock in packs, which helps you check your total. Leave a line empty if you did not count it, and it will not change. Enter 0 for a batch that is not on the shelf at all. Click Save progress as you go, so a power cut during load-shedding does not cost you the work.
After saving, each line shows OK, a plus for extra stock or a minus for a shortage. When you are happy, click Save & post. MediPOS creates one stock adjustment with the reason Count correction for every line with a difference. It is valued at each batch's cost and booked to Stock count differences, kept apart from breakage and expiry losses. If everything matched, MediPOS tells you the shelf matched the system. Losses you can explain before the count, such as a broken bottle or an expired strip, go in as their own stock adjustment with a reason like Damaged / broken or Expired write-off, so the count only has to explain what is left.
The trail stays. The audit log records Stock count posted with how many lines were counted and how many had differences, and a posted count cannot be edited or undone. A line counted wrongly is fixed with a new stock adjustment, and a box the system never knew about is added with the Found stock reason. Only people with the Run stock counts permission can start and post counts, so give it to people you trust. This is how MediPOS pharmacy inventory software keeps the shelf and the books in agreement. Whether Stock counts is in your menu depends on your plan, and the pricing page shows which plans include it.
Common questions
Do I have to count the whole shop at once?
No. Count one rack or one group of products at a time. In MediPOS, lines you leave empty are ignored when you post, so a partial count is safe.
Should I count sealed boxes one by one?
A sealed box can be counted as full, in base units. Open boxes, loose strips and single tablets need a proper count.
What if the power goes in the middle of a count?
On paper, nothing is lost. In MediPOS, whatever you saved with Save progress is kept, and you can carry on later or the next day.
Related reading
Founder & CEO, Innobrains Technologies
Arshad Ali is the founder and CEO of Innobrains Technologies, the company that makes MediPOS: pharmacy POS and management software built for medical stores in Pakistan.
Run your pharmacy on MediPOS
Billing, batch and expiry stock, distributor schemes, udhaar and reports — on your shop PC without internet, or in the cloud. Free for 14 days, no card needed.
Related articles
Why medical stores lose money on expired medicines, and a routine that stops it
Expired stock is cash thrown in the bin. Here is why medicines expire on the shelf, a weekly and monthly routine that catches them in time, and why batch records at purchase are what make returns to the distributor possible.
25 Sep 2026 · 8 minFEFO vs FIFO: which batch should your pharmacy sell first?
FIFO sells what arrived first. FEFO sells what expires first. A worked example with two batches of the same syrup shows why the difference matters in a medical store, and what your shelves and records need to get it right.
25 Sep 2026 · 8 minManaging udhaar in a pharmacy without losing money or customers
Udhaar keeps regular customers coming back, but unrecorded credit quietly eats your cash. A practical guide to limits, records, statements, polite collection and old balances.
25 Sep 2026 · 8 min