Using bioinks for 3D bioprinting of cellular constructs remains a challenge due to factors including viscosity, fluid dynamics and shear stress. The encapsulation of cells within the bioinks directly affects the quality of 3D bioprinting and microfluidic pumping is a commonly used supporting approach. The accuracy of microfluidic pumps can be further improved by introducing various mixing techniques. However, many of these techniques introduce complex geometries or external fields. In this study, we used a simple control technique of time-dependent pulsing for instant gelation of the peptide bioinks and observed its effect during the bioprinting process. Various time-dependent periodic signals are imposed on to a stable flow cycle and the effects are analyzed. The microfluidic pumps are programmed with different flow patterns represented by low frequency sinusoidal pulses, ramp inputs, and duty cycle pulses. Different combinations of these pulses are tested to achieve an optimal pulse for improved quality of printed constructs. Time-varied pulsing of microfluidic pumps, particularly as square waveforms, is found to provide better continuous flow and avoid material buildup within the extruder unit when compared to pumping at a constant flow rate with manual tuning. Clogging is avoided since the gelation rate is periodically reduced which avoids gel clumps in the printed constructs. This study substantially improves the use of suitable peptide bioinks, standardizes the 3D bioprinting process, and reduces clogging and clumping during printing. Our findings allow for printing of more accurate and complex constructs for applications in tissue engineering, such as skin grafting, and other regenerative medical applications.