Renewable energy needs are steadily on the rise. Bidirectional DC/DC converters are essential in charging and discharging various storage batteries, such as PV/ESS (photovoltaic/energy storage system). A dual active bridge (DAB) converter, in particular, transfers power in both directions by phase shift using a soiled state transformer (SST). To reduce switching inrush current in batteries under high voltages, a soft start-up is demonstrated during the initial switching operation. When a supercapacitor (SC) is used as a battery, the reverse power caused by the inrush current appears under high voltage at the DC-link side. This causes serious electrical damage to the PV/ESS’ boost converter and inverter. To suppress peak overshoot voltage and stabilize soft start-up transients, we propose a three-step soft start-up controller and algorithm for bidirectional DAB converter implementation at virtual ESS and UPS. The step-by-step control strategy by OLDC (open loop duty control), OLPSC (open loop phase shift control), and OLFC (open loop frequency control) provides a stable soft start-up operation. In the initial stage of the OLDC, the duty ratio is gradually increased by the PWM (Pulse width modulation) signal. In the middle stage, a phase difference is seen as per the voltage of the SC. The OLPSC is performed to reduce the phase difference. In the final stage, the OLFC is performed to smoothly control the small phase difference. The overshoot or inrush current is drastically suppressed toward the DC-link and SC module. Consequently, we demonstrate a proposed controller and algorithm with prototype 5 kW DAB converter.