Recently, evidence was provided for the existence of an $a$-function for renormalisable quantum field theories in three dimensions. An explicit expression was given at lowest order for general theories involving scalars and fermions, and shown to be related to the beta-functions by a gradient flow equation with positive-definite metric as in four dimensions. Here, we extend this lowest-order calculation to a general abelian Chern-Simons gauge theory coupled to fermions and scalars, and derive a prediction for part of the four-loop Yukawa beta-function. We also compute the complete four-loop Yukawa beta-function for the scalar-fermion theory and show that it is entirely consistent with the gradient flow equations at next-to-leading order.