Each level in Body Harvest requires the player to stop the aliens from slaughtering everyone in the shield area. The player will navigate the map, usually coming across towns where aliens will teleport in to attack the town.
Gameplay consists of completing a series of missions. Many of these are very basic i.e. reach a certain area, but others can be more complicated and require some thought and/or skill. Once one completes a mission they are then prompted to check the map to find out what the next mission is.
There is a meter at the bottom of the screen that represents civilian casualties. If too many civilians die for any reason, the aliens will destroy the area. Mostly, only Harvester aliens will deliberately kill people, so the player must destroy Harvester waves as they progress throughout the level. There are also some optional missions that require saving people from the aliens. Although one can fail these missions and still progress through the game, doing so usually results in significant human casualties.
The use of vehicles is a key aspect of this game. Vehicles are needed to face off with aliens and specific vehicles are often required to complete missions. These vehicles include cars, tanks, boats, planes, helicopters, and even a flying saucer. In addition the Alpha I (the ship the player uses to travel through time) becomes a powerful hovercraft during boss battles and for the entirety of the Comet level.
Each level is divided into stages and the shield portal to the next stage only opens once the player has destroyed that stages Alien processor.
The goal of each level is to destroy the Shield Generator that creates the shield that surrounds each level. As soon as this occurs the player faces the level's boss.