An automated sequential reaction system that can be used to either sequentially produce a plurality of different products each requiring a single reaction, or to produce a desired product that requires a series of sequential reactions. A system controller controls an automated reactant supply, a solvent supply, a reaction module, a detector, and a product collector. Prior to initiating any reaction, the system is flushed with solvent and a heat exchanger supplies the reaction module with a temperature-conditioned fluid to maintain the reaction module at a desired temperature. For single reactions, a plurality of reactants are injected into a chemical reactor included in the reaction module. As fluid exits the chemical reactor, the detector determines if the fluid is a desired chemical product or solvent, and routes the fluid to the appropriate receptacle. Once a predetermined volume of a desired product is obtained, the system is flushed with solvent, and a different set of reactants are injected into the chemical reactor to produce the next desired product. The process is repeated until a substance library of the desired products is obtained. For products requiring sequential reaction steps, either a plurality of reactors are employed, or an intermediate product produced by a previous reaction is reintroduced into the reaction module with an appropriate reactant to complete the next sequential reaction.