For most Australian Shopify merchants, the end of financial year is two things happening at once: a genuine sales opportunity, because shoppers are primed for EOFY deals, and a compliance deadline, because your books need to close cleanly on 30 June. Treat it as only the first one and you end up with a messy stocktake, a BAS that doesn’t reconcile, and a sale that quietly ate more margin than you realised.
This isn’t a generic “run a June sale” article. It’s specifically about what changes inside your Shopify admin, discounts, inventory, tax settings, reporting, when EOFY and GST obligations land in the same few weeks. We’ll walk through the store-side setup, the stocktake and reporting basics every GST-registered merchant should be across, and a checklist you can work through in the lead-up to 30 June.
One caveat up front: GST registration thresholds, BAS lodgement cycles and specific tax figures depend on your business structure and turnover, and they do get updated. Nothing in this article should be read as tax advice, for anything specific to your numbers, confirm with your accountant or check the current rules on the ATO website. What we can speak to with confidence is how Shopify itself handles discounting, inventory and reporting, because that’s the part we work with directly.
Why EOFY Is Different From a Normal Shopify Sale
A Black Friday or Christmas sale is primarily a marketing event. EOFY is a marketing event layered on top of an accounting deadline, and that changes a few things about how you should approach it in Shopify:
- Timing is fixed and non-negotiable. Your sale has to start and end around 30 June, not whenever traffic looks good. That means discount scheduling in Shopify, not manual price changes, is the safer approach.
- Stock movement during the sale affects your stocktake. If you’re doing a physical or reconciled stock count around 30 June, a high-velocity sale in the same window makes that count harder to get right unless you plan the sequencing.
- Your reporting needs to be BAS-ready, not just sales-ready. A normal sale report tells you revenue and units sold. An EOFY report needs to cleanly show GST collected, which is what your BAS (Business Activity Statement) draws from.
- You’re often clearing aged or excess stock, not just driving volume, which changes how you should price and which products you put on sale.
None of this means EOFY prep is complicated. It means the order you do things in matters more than usual.
Get Your Numbers Foundation Right First
Before you touch a single discount code, it’s worth confirming the basics are actually set up correctly in Shopify. This is the part merchants skip when they’re focused on the sale campaign, and it’s the part that causes the most pain in July.
Check your GST settings are accurate
If you’re GST-registered, go to Settings > Taxes and duties > Australia in your Shopify admin and confirm GST is correctly applied at the standard rate to taxable products, and that any GST-free items (if you sell any, such as certain food or health products) are correctly flagged as tax-exempt at the product level. This matters more at EOFY because any error here compounds across every sale transaction in the period your BAS is about to report on. Whether you’re registered for GST at all, and how often you need to lodge a BAS (monthly, quarterly or annually), depends on your turnover and business circumstances, your accountant or the ATO can confirm exactly where you sit.
Understand your stocktake obligations
Most Australian businesses that hold trading stock need to account for it at year end, broadly, working out the value of stock on hand at 30 June for your tax return. Exactly how this applies to your business (including any simplified rules that might apply based on your turnover) is again something to confirm with your accountant, but from a Shopify operations standpoint, you need:
- An accurate inventory count method (physical count, cycle count, or a Shopify POS-assisted count if you sell in person too)
- Inventory levels in Shopify that actually reflect what’s on the shelf, not what the system thinks after months of manual adjustments, damages, and unlogged returns
- A clear cut-off point, so stock movements from your EOFY sale are counted on the right side of 30 June
Reconcile Shopify Payments payouts against your bank
Before you close the books, pull your payout reports (Settings > Payments > View payouts, or Finance > Payouts in the newer admin) and check they match what’s landed in your bank account. Payout timing lags behind order dates, an order placed on 29 June might not pay out until early July, so this is a common source of confusion when reconciling revenue to the correct financial year. Flag this pattern for your bookkeeper rather than trying to force every order into the period it was placed in.
Setting Up Your EOFY Sale in Shopify
Once the numbers foundation is solid, the sale itself is mostly a discounting and scheduling exercise inside Shopify.
Automatic discounts vs discount codes
Shopify gives you two discount types under Discounts in the admin:
- Automatic discounts apply at checkout with no code needed, good for a sitewide EOFY sale you want frictionless.
- Discount codes require the shopper to enter a code, better if you’re running a targeted offer (e.g. an email-only EOFY code for existing customers) alongside a broader sitewide markdown.
You can run both at once, but check your combination settings on each discount so they don’t unintentionally stack. Nothing erodes an EOFY sale’s margin faster than a 20% automatic discount stacking with a 15% code because combinations weren’t restricted.
Schedule start and end dates and times, and check the timezone
Set your sale’s start and end date/time directly in the discount setup rather than manually changing prices and reverting them. This avoids the classic mistake of forgetting to switch a sale off, which either bleeds margin into July or creates a pricing error when a “was/now” price stops making sense. Double-check your Shopify store’s timezone setting (Settings > General) matches AEST/AEDT as expected, a mismatched timezone can mean your “ends 30 June” sale actually cuts off hours early or late for your actual customers.
Decide what you’re actually discounting, and why
An EOFY sale works best when it does one of two jobs clearly:
- Clears genuinely aged or excess stock, useful for both cash flow and simplifying your stocktake, since you’re moving stock you’d otherwise have to count and value at year end anyway.
- Drives a straightforward, sitewide “EOFY sale” moment that matches customer expectations around this time of year, even on newer stock.
Trying to do both with one blanket discount usually means you either discount healthy-margin new stock unnecessarily, or don’t discount aged stock enough to actually move it. It’s worth pulling a sales-by-product report first (Analytics > Reports) to identify genuinely slow-moving SKUs and building a tiered discount structure around them rather than a single flat percentage off everything.
Update product pages and collections before the sale goes live
Build (or update) an EOFY collection, make sure sale badges or countdown elements in your theme are actually wired up if you’re using them, and check that any “compare at price” fields you’re relying on to show strikethrough pricing are set correctly, this is a common spot for errors when discounts are applied at the cart/checkout level rather than the product level, since the product page won’t show a strikethrough unless compare-at price is also set.
The EOFY Shopify Prep Checklist
Work through this in roughly this order, ideally starting 3-4 weeks out from 30 June:
- Confirm GST settings in Settings > Taxes and duties are correct for every product type you sell.
- Talk to your accountant or bookkeeper about your BAS lodgement cycle and any stocktake requirements specific to your business.
- Run a sales-by-product report to identify aged or slow-moving stock worth prioritising in the sale.
- Decide your discount structure, sitewide flat discount, tiered by category, or targeted clearance on specific SKUs.
- Set up discounts in Shopify with correct combination settings, start/end dates, and confirmed timezone.
- Update compare-at pricing on product pages so strikethrough pricing displays correctly, if your theme relies on it.
- Plan your stocktake cut-off, decide exactly when the count happens relative to the sale’s end date.
- Reconcile Shopify Payments payouts against your bank statements for the period.
- Export your finance and tax reports (Analytics > Reports > Finances, and the Taxes finance report) ahead of your BAS.
- Switch off or expire the sale on schedule and confirm compare-at pricing reverts cleanly.
Common Mistakes We See Around EOFY
A few patterns come up repeatedly when Shopify merchants rush EOFY prep:
- Running the stocktake mid-sale, which means the count doesn’t reflect a stable inventory position and has to be redone or adjusted after the fact.
- Leaving GST misapplied on a handful of products for months, which only gets noticed when the BAS numbers don’t reconcile.
- Forgetting subscription-based app charges that renew in June, which affects both cash flow timing and expense reporting for the year.
- Discounting without checking margin on freight-inclusive pricing, if you offer free or flat-rate shipping, a deep discount can push some orders close to break-even once shipping cost is factored in.
- Not exporting reports before archiving or changing app data, some apps only retain detailed historical data for a limited window, so pulling your EOFY reports promptly is worth doing rather than assuming you can go back for them in August.
When to Bring in a Specialist
Most of what’s above is manageable in-house if your store isn’t especially complex. Where it’s genuinely worth getting outside help is when your GST setup involves mixed taxable and GST-free products, multiple sales channels (online plus wholesale or in-person via POS), or when you’ve simply never been fully confident your Shopify tax settings were correct in the first place. A one-off review before EOFY is far cheaper than untangling a BAS discrepancy after the fact.
This is exactly the kind of check covered in our Shopify GST setup guide, which walks through how GST should be configured across products, shipping and any B2B pricing in your store. If you’d rather have someone look directly at your store’s setup, a Shopify audit can flag tax, inventory and reporting issues alongside the usual technical and SEO checks.
FAQ
Do I need to run an EOFY sale on my Shopify store?
No, it’s optional. Many Australian merchants run one because customer expectations around this time of year make it a reliable sales window, and because it’s a convenient moment to clear aged stock before a stocktake. If your margins are thin or you don’t have excess stock to move, a smaller, more targeted offer can work just as well as a sitewide markdown.
How do I make sure my Shopify GST settings are correct before EOFY?
Check Settings > Taxes and duties > Australia and confirm the tax status of each product type matches how it should be treated (standard-rated or GST-free, if applicable). If you’re unsure whether your setup is correct, it’s worth a dedicated review rather than assuming it’s right, misapplied tax on even a few products can complicate your BAS.
Should I schedule my EOFY sale to end exactly at midnight on 30 June?
That’s a common approach, but the important part is checking your Shopify store’s timezone setting matches your business location, so “midnight 30 June” in the admin actually lines up with midnight for your customers and your own reporting cut-off.
Can Shopify help with my stocktake, or do I need a separate app?
Shopify’s native inventory tracking can support a stocktake if your stock levels have been kept accurate, and Shopify POS has stock count tools if you sell in person. For larger or more complex inventories, a dedicated inventory or stocktake app can make the count faster and more accurate, but the app is only as good as how consistently your inventory has been tracked throughout the year.
What’s the difference between a BAS and my EOFY tax return, and does it affect my Shopify sale planning?
A BAS reports GST (and other obligations) over a shorter reporting period, monthly, quarterly or annually depending on your setup, while your annual tax return covers the full financial year. Your EOFY sale itself doesn’t need to be timed around either one, but the accuracy of your GST settings and sales records affects both, which is why getting the store-side setup right before the sale matters.
Ready to Get Your Store EOFY-Ready?
If you’re not fully confident your GST settings, discounting setup or reporting are in good shape before 30 June, it’s worth getting a second set of eyes on it now rather than in the middle of BAS season. Book a call with our team and we’ll help you get your Shopify store sale-ready and compliance-ready at the same time.
