Can I buy the real estate separately from the operating business itself?

Yes, this is a common and often deliberate structure. You can purchase the operating business — as shares or assets — while buying the real property under a separate purchase agreement, sometimes from a different owning entity or from the seller personally if the property was never inside the operating corporation to begin with.

The nuance is that real property transactions carry their own distinct requirements regardless of how the rest of the deal is structured. Ontario land transfer tax applies to the conveyance of the real estate specifically, calculated separately from whatever GST/HST or capital-gains treatment applies to the operating business portion. If the property is currently owned by the same corporation whose shares or assets you're buying, separating it out first may require its own transfer or reorganization step before your purchase closes, with its own tax consequences to plan for.

Buying the real estate separately can also simplify future flexibility — you might want to lease the property back to the operating business rather than tying its ownership to your operating risk. A business lawyer can structure the two purchases together, and confirm the land transfer tax and any reorganization steps are properly accounted for before closing.