Does selling inventory as part of the deal get taxed differently than selling goodwill?

Yes, quite differently. Inventory sold as part of a business is generally treated as a sale in the ordinary course of business for tax purposes, so the amount by which the sale price exceeds its cost is taxed as ordinary business income, fully includible, not as a capital gain. Goodwill, by contrast, is a capital property, so any gain on its sale is a capital gain, only half of which is generally taxable, benefiting from more favourable treatment than inventory's full-income treatment.

Because of this gap, how much of the purchase price gets allocated to inventory versus goodwill affects the seller's total tax bill meaningfully, separate from the equipment-and-recapture issues that come up elsewhere in the same deal. Inventory is also usually valued and negotiated somewhat separately from the rest of the purchase price, often based on an agreed valuation method (cost, or a discount to reflect obsolete or slow-moving stock) rather than simply being folded into a single lump-sum figure.

Because inventory sales generally attract HST in the same way most tangible goods do (unless the whole sale qualifies for the going-concern election), confirming how inventory is being valued and taxed as its own line item, rather than assuming it's treated the same as goodwill, protects against surprises on both fronts.