High production of biodiesel results in a surplus of glycerol as a byproduct that leads to a drastic decline in the glycerol price as well as overall biodiesel production. Alternative methods must be introduced for the economical process for biodiesel production via utilization of crude glycerol into valuable chemicals or fuel additives. This study introduces an ecofriendly process of solketal synthesis from glycerol and acetone in the presence of a novel metakaolin clay catalyst, which is a useful additive in biodiesel or gasoline, in order to enhance the octane number and to control the emissions. Moreover, kaolin clay catalysts are low cost, abundantly available, eco-friendly and one of the more promising applications for solketal synthesis. In this study, raw kaolin clay was activated with an easy acid activation technique, modification in physicochemical and textural properties were determined by using X-ray diffraction (XRD), Fourier Transform Infra-Red (FTIR) spectroscopy, Brunauer–Emmett–Teller (BET) and Field Emission Scanning Electron Microscope. Among all acid-treated catalysts, metakaolin K3 have shown best catalytic properties, high surface area and pore size after acid activation with 3.0 mol/dm3 at 98 °C for 3 h. Acetalization of glycerol with acetone carried out in the presence of an environmentally friendly and inexpensive novel metakaolin K3 catalyst. The maximum yield of solketal obtained was 84% at a temperature of 50 °C, acetone/glycerol molar ratio 6/1 and for 90 min with novel metakaolin clay catalyst. Effect of various parameters (time, temperature, acetone/glycerol molar ratio, catalyst loading) on the solketal yield and glycerol conversion was discussed in detail. This approach offers an effective way to transform glycerol into solketal—a desirable green chemical with future industrial applications.