In this article, we propose a fully-discrete scheme for the numerical solution of a nonlinear time-fractional biharmonic problem. This problem is first converted into an equivalent system by introducing a new variable. Then spatial and temporal discretizations are done by the weighted $b$-spline method and $L2$-$1_\sigma$ approximation, respectively. The weighted $b$-spline method uses weighted $b$-splines on a tensor product grid as basis functions for finite element space and by construction, it is a mesh-free method. This method combines the computational benefits of $b$-splines and standard mesh-based elements. We derive $\alpha$-robust \emph{a priori} bounds and convergence estimate in the $L^2(\Omega)$ norm for the proposed scheme. Finally, we carry out few numerical experiments to support our theoretical findings.