<p>We study Kupershmidt operators, Nijenhuis operators, and Kupershmidt-Nijenhuis structures on finite-dimensional pre-Malcev algebras over a field of characteristic zero. We construct several new families of complex pre-Malcev algebras that are not pre-Lie algebras in dimensions two, three and four. We use the compatibility of linear operators to establish connections between Kupershmidt operators, Nijenhuis operators and Kupershmidt-Nijenhuis structures on pre-Malcev algebras. Moreover, we use a method from computational ideal theory to characterize the geometric structures of the varieties of Kupershmidt operators and Nijenhuis operators on a three-dimensional complex pre-Malcev algebra.</p>