Method for controlling a microfluidic device which comprises a matrix of microfluidic capsules and channels linking the microfluidic capsules to one another, each microfluidic capsule being able to be controlled between a first state in which it can be filled with a fluid and a second state in which it is empty, blocking the passage of said fluid, said matrix comprising: - at least one first reservoir (Ra) intended to receive a first fluid and one second reservoir (Rb) intended to receive a second fluid to be mixed with the first fluid, - said microfluidic capsules comprising so-called mixing microfluidic capsules, so-called isolation microfluidic capsules and so-called mixing-isolation capsules, - at least two series of capsules called first filling series and second filling series, - the first filling series comprising the first reservoir and one or more mixing capsules, the second filling series comprising the second reservoir and one or more mixing capsules, - each reservoir being separated from a first mixing capsule of its series by an isolation capsule, - in each filling series, each mixing capsule being separated from another mixing capsule of the series by an isolation capsule, - at least one mixing capsule of the first filling series being separated from another mixing capsule of the second filling series by a mixing-isolation capsule by forming a series of capsules, called mixing series, said method being characterized in that it comprises: - an initialization phase in which: o the mixing microfluidic capsules and the isolation microfluidic capsules situated in each filling series are set to their first state so as to be each filled, respectively by the first fluid and by the second fluid present in their associated reservoir, each mixing-isolation capsule being in its second state, o the isolation capsules are set to their second state so as to isolate, in each filling series, the mixing capsules from one another, - a mixing phase in which the first fluid present in a mixing capsule of the first filling series is mixed with the second fluid present in a mixing capsule of the second filling series through a mixing-isolation capsule. - at least one first reservoir (Ra) intended to receive a first fluid and one second reservoir (Rb) intended to receive a second fluid to be mixed with the first fluid, - said microfluidic capsules comprising so-called mixing microfluidic capsules, so-called isolation microfluidic capsules and so-called mixing-isolation capsules, - at least two series of capsules called first filling series and second filling series, - the first filling series comprising the first reservoir and one or more mixing capsules, the second filling series comprising the second reservoir and one or more mixing capsules, - each reservoir being separated from a first mixing capsule of its series by an isolation capsule, - in each filling series, each mixing capsule being separated from another mixing capsule of the series by an isolation capsule, - at least one mixing capsule of the first filling series being separated from another mixing capsule of the second filling series by a mixing-isolation capsule by forming a series of capsules, called mixing series, - an initialization phase in which: o the mixing microfluidic capsules and the isolation microfluidic capsules situated in each filling series are set to their first state so as to be each filled, respectively by the first fluid and by the second fluid present in their associated reservoir, each mixing-isolation capsule being in its second state, o the isolation capsules are set to their second state so as to isolate, in each filling series, the mixing capsules from one another, o the mixing microfluidic capsules and the isolation microfluidic capsules situated in each filling series are set to their first state so as to be each filled, respectively by the first fluid and by the second fluid present in their associated reservoir, each mixing-isolation capsule being in its second state, o the isolation capsules are set to their second state so as to isolate, in each filling series, the mixing capsules from one another, - a mixing phase in which the first fluid present in a mixing capsule of the first filling series is mixed with the second fluid present in a mixing capsule of the second filling series through a mixing-isolation capsule.