Blueberry pomace is a rich source of high-value bioactive polyphenols with presumed health benefits. Their incorporation into functional foods and health-related products benefits from coencapsulation and protection of polyphenol-rich extracts in suitable carriers. This study aimed to create a water-in-oil-in-water (W1/O/W2) double emulsion system suitable for the coencapsulation of total phenolics (TP) and anthocyanins (TA) from a polyphenol-rich extract of blueberry pomace (W1). The effect of critical physical parameters for preparing stable double emulsions, namely homogenization pressure, stirring speed and time, was investigated by measuring the hydrodynamic diameter, size dispersity and zeta potential of the oil droplets, and the encapsulation efficiency of TP and TA. The oil droplets were negatively charged (negative zeta potential values), which was related to the pH and composition of W2 (whey protein isolate solution) and suggests stabilization by the charged whey proteins. Increasing W1/O/W2 microfluidization pressure from 50 to 200 MPa or homogenization speed from 6000 to 12,000 rpm significantly increased droplet diameter and zeta potential and decreased TA and TP encapsulation efficiency. Increasing W1/O/W2 homogenization time from 15 to 20 min also increased droplet diameter and zeta potential and lowered TA encapsulation efficiency, while TP encapsulation did not vary significantly. In contrast, increasing W1/O homogenization time from 5 to 10 min at 10,000 rpm markedly increased TA encapsulation efficiency and reduced droplet diameter and zeta potential. High coencapsulation rates of blueberry polyphenols and anthocyanins around 80% or greater were achieved when the oil droplets were relatively small (mean diameter < 400 nm), with low dispersity (<0.25) and a high negative surface charge (−40 mV or less). These characteristics were obtained by homogenizing for 10 min at 10,000 rpm (W1/O), then 6000 rpm for 15 min, followed by microfluidization at 50 MPa.