The hardest thing when starting an e-commerce business is coming up with a product that is marketable. This entails finding an unmet need or a need that has not been met sufficiently and then fulfilling that need within a budget that will enable you to function before selling any products.
After this, the next top challenges include:
Manufacturing at a good cost or finding cost-effective suppliers
Finding cost-effective warehousing
Effectively managing your inventory
Staying on top of all the bureaucracy required to run an online business including taxes, licenses and registrations
Generating leads or customers
Optimizing your marketing ROI
Excelling at customer support
Re-engaging your customers