We explore memory effects for novel Kundt wave spacetimes in the recently proposed Eddington-inspired Born-Infeld (EiBI) theory of gravity. First, we construct new, exact Kundt wave geometries in this theory for two different matter sources--(i) generic matter designed to satisfy the field equations as well as energy conditions, and (ii) electromagnetic field. For both sources we find that the EiBI theory parameter $\kappa$ couples only with the nonradiative part of the physical metric solution. Thereafter, we solve the geodesic and the geodesic deviation equations, in the above spacetimes with the aim of arriving at memory effects. This analysis is carried out numerically and reveals unique memory features depending on the type of matter source present and the signature of the spacetime scalar curvature. The role of $\kappa$ in influencing the memory effect, for a given background spacetime, is also noted. Thus, apart from providing novel radiative solutions in EiBI gravity, we also show how different matter configurations are responsible for distinct memory characteristics.