A process and system for separating and upgrading bio-oil into renewable fuels is provided. The process comprises separating bio-oil into a light fraction, an optional intermediate fraction, and heavy fraction based on their boiling points. The light fraction and optional intermediate fraction can be upgraded via hydrotreatment to produce a renewable gasoline and a renewable diesel, which may be combined with their petroleum-derived counterparts. The heavy fraction may be subjected to cracking and further separated into light, intermediate, and heavy fractions in order to increase the yield of renewable gasoline and renewable diesel.