An apparatus and method are provided for filling multi-chamber containers with different loose bulk materials. The apparatus and method may be particularly well-suited to packaging at least one bulk material, which is susceptible to water, chemicals, or other contaminants, with at least one other bulk material. The apparatus is a machine that includes separate hoppers for handling the separate bulk materials, and directs the separate bulk materials into different chambers of a multi-chamber container, which is then transported away from the machine for storage or use. The machine may include one or more movable hoppers supported on tracks, for moving the bulk materials to the hoppers that direct the bulk materials into different chambers of the multi-chamber container. A controller and data logger may be provided to control the apparatus and record the quantity and/or weight of the contents of each multi-chamber container.