For binary recurrence sequences, \(\left( y_{k} \right) _{k \in \mathbb {Z}}\) , arising from the solutions of generalised Pell equations, \(X^{2}-dY^{2}=c\) , where \(y_{0}\) is any positive square and \(c=-2^{\ell }p^{m}\) for an odd prime, p, and non-negative integers \(\ell \) and m, we show that there are at most 4 distinct squares with \(y_{k}\) sufficiently large. From this result, we also show that there are at most 7 distinct squares when \(y_{0}=1,2^{2},\ldots ,7^{2}\) , or once d exceeds an explicit lower bound, without any conditions on the size of such squares.