An automated multi-step chromatography purification system arranged to perform a plurality of isolated multi-step purification cycles for purifying a target molecule from a feed source (406a to e), comprising: • system controller comprising a memory storing instructions for controlling the components of the system, • two or more purification sections (410,415,420), each representing a purification step, • at least one pump for driving the purification, • a valve arrangement with two or more valves (407,411a,b,421a,b) for controlling the fluid flow in the system wherein: one of the purification sections is a capture section with two or more capture columns (412a-c), wherein the valve arrangement comprises at least one pair of multi-port valves (411a, 411b), and the at least one pair of multi-port valves of the valve arrangement is arranged for alternately connecting each capture column (412a-c): a) to a capture flow path, wherein a first valve of the at least one pair of multi-port valves (411a, 411b) fluidically connects the alternately connected capture column (412a-c) to a feed source (406a-e) for capturing the respective target molecule, and b) to an eluent purification flow path, wherein a second valve of the at least one pair of multi-port valves (411a, 411b) fluidically connects the alternately connected capture column (412a-c) to a subsequent purification section (415, 420) for carrying eluted captured target molecule to a subsequent purification section subsequent to the capture section and for preparing one of the columns for a subsequent capture phase, wherein: the subsequent purification section comprises a smaller number of eluent purification flow paths compared to the number of capture columns, each eluent purification flow paths comprising a purification column, and whereby eluent flow from the capture section is sequentially purified in said eluent purification flow paths with intermediate cleaning of those eluent purification flow paths to keep subsequent purifications isolated, wherein each purification section is in direct fluidic communication with the subsequent purification section without any intermediate sample storage component. • system controller comprising a memory storing instructions for controlling the components of the system, • two or more purification sections (410,415,420), each representing a purification step, • at least one pump for driving the purification, • a valve arrangement with two or more valves (407,411a,b,421a,b) for controlling the fluid flow in the system one of the purification sections is a capture section with two or more capture columns (412a-c), wherein the valve arrangement comprises at least one pair of multi-port valves (411a, 411b), and the at least one pair of multi-port valves of the valve arrangement is arranged for alternately connecting each capture column (412a-c): a) to a capture flow path, wherein a first valve of the at least one pair of multi-port valves (411a, 411b) fluidically connects the alternately connected capture column (412a-c) to a feed source (406a-e) for capturing the respective target molecule, and b) to an eluent purification flow path, wherein a second valve of the at least one pair of multi-port valves (411a, 411b) fluidically connects the alternately connected capture column (412a-c) to a subsequent purification section (415, 420) for carrying eluted captured target molecule to a subsequent purification section subsequent to the capture section and for preparing one of the columns for a subsequent capture phase, a) to a capture flow path, wherein a first valve of the at least one pair of multi-port valves (411a, 411b) fluidically connects the alternately connected capture column (412a-c) to a feed source (406a-e) for capturing the respective target molecule, and b) to an eluent purification flow path, wherein a second valve of the at least one pair of multi-port valves (411a, 411b) fluidically connects the alternately connected capture column (412a-c) to a subsequent purification section (415, 420) for carrying eluted captured target molecule to a subsequent purification section subsequent to the capture section and for preparing one of the columns for a subsequent capture phase, wherein: the subsequent purification section comprises a smaller number of eluent purification flow paths compared to the number of capture columns, each eluent purification flow paths comprising a purification column, and whereby eluent flow from the capture section is sequentially purified in said eluent purification flow paths with intermediate cleaning of those eluent purification flow paths to keep subsequent purifications isolated, wherein each purification section is in direct fluidic communication with the subsequent purification section without any intermediate sample storage component.