This article is written by guest contributor Tom Moore, Director, R&D and Government Incentives at BlueRock.

Growth is an adventure, but once your business starts scaling, indirect taxes can quickly go from an afterthought to a minefield. Whether you’re claiming R&D tax incentives, exploring cross-border operations or managing a headcount surge, tax issues tend to sneak up and bite just when you’re building momentum.

Here’s how some key indirect tax risks can play out for ambitious, scaling firms and why it pays to get ahead of them.

R&D Tax Incentives

Australia’s R&D tax incentive can be a real lifeline for cash flow, but complexity and fine print has tripped up many a first-time founder.

The nuances between ‘core’, ‘supporting’ and ineligible activities are often misunderstood, and businesses frequently fall foul of the rules because they’re missing documentation or claiming ineligible projects. The ATO is dialling up scrutiny too, especially for digital technology claims. You need tight records and a clear link between what you claim and what your team actually develops.

R&D consultants can help you jump through the hoops, set up your processes right from the start, and avoid the nightmare scenario where you’re asked to repay incentives years later.

Transfer Pricing

If you’ve got any international touchpoints (such as offshore entities, cross-border IP, or founders working across borders) the ATO’s transfer pricing rules may apply, regardless of whether you’re currently profitable. Establishing defensible pricing between related parties, properly documenting inter-company loans and ensuring royalties or management fees reflect commercial terms – not “mate's rates”, can be critical to your tax position.  Missteps here can lead to increased taxation, audits or complications during funding rounds and exists.

Scaling businesses evolve fast. What worked in a founder-led setup won’t hold up once you reach a significant size or attract external investment.

If global expansion is on your roadmap, early conversations about transfer pricing can save you time, money and undue stress.  

Payroll Tax Risks

Once a business starts operating across states or blending employees and contractors, payroll tax stops being a box-ticking exercise and becomes something that needs to be managed. Grouping rules, changing thresholds and state-by-state differences make it all too easy to get caught out, while “set and forget” approaches rarely work with a growing team.

The classic traps? Not registering when stepping into a new state, misclassifying contract arrangements, or missing new rules about remote staff and deemed employees. The result: back taxes, penalties, and a compliance hangover just when you least expect it.

A practical approach is to run payroll compliance reviews and keep a sharp eye on contractor versus employee status as your workforce model evolves.

Reducing Super Guarantee Charge (SGC) Risks

The consequences of late or unpaid super can be devastating. Think director penalty notices, penalties up to 200%,unlimited amendment periods, denied tax deductions, and interest charges theATO won’t remit. The kicker? Even being just one day late is enough to trigger these penalties.

Employers need to understand the details: many commercial clearing houses need up to 10 business days to process payments, so you’ve got to leave enough time for super to reach the fund.

It’s also vital to get your calculations right. Check every employee’s award and remember that “ordinary time earnings” (OTE) can trip you up, especially when dealing with bonuses, overtime or different contract arrangements. Some workers are treated as employees under the super rules even if they’re genuinely contractors. This includes anyone paid for gigs, events or promotions, so businesses using influencers, performers, or speakers can’t afford to assume they’re in the clear.

Early SGC intervention is crucial.

If a business can’t pay super on time, the reality is it can’t afford to pay super late either. The penalties and interest are that harsh. Not only can nominal interest rack up from the very start of the quarter, but SGC shortfalls are calculated on all salary and wages, which is often more than you’d expect.

Reallocating late payments or trying for a late payment offset can get complicated fast and, if handled incorrectly, you could even end up needing to pay twice for the same quarter. The ATO has shown they’ll grant remission for penalties in some cases (BlueRock’s tax advisory team has negotiated reductions from over $1 million), but it’s much easier and cheaper to proactively manage super obligations from the start, rather than fix problems after they’ve snowballed.

Professional tax advice might save you more than money

Fast growth is great, but scaleup success often brings compliance risk, and many tax mistakes only show up months or years later. Founders who act early, and not just on compliance, can unlock available incentives and avoid hidden costs.

Paying for specialist tax advice can be a wise investment, as “tick-the-box” approaches to tax can trip you up when you’re scaling or attracting investors. A quick, proactive review with BlueRock’s advisory team (in conjunction with Mighty Partners’ funding expertise) will help ensure sustainable growth and peace of mind.