Methods, systems and apparatus for error correction of fermionic quantum simulation. In one aspect, a method includes representing a fermionic system as a graph of vertices and edges, where each vertex represents a fermionic system fermionic mode and each edge represents an interaction between two respective fermionic modes; allocating a qubit to each edge in the graph to form a qubit system; determining qubit operators that satisfy a set of fermionic commutation and dependence relations, where the qubit operators are non-uniform with respect to the graph vertices; determining stabilizer operators corresponding to products of quadratic Majorana operators on respective loops in the graph, where a common eigenspace of the defined stabilizer operators defines a code subspace that encodes states of the fermionic system to be simulated; and simulating the fermionic system by evolving the qubit system under a qubit Hamiltonian that includes the determined qubit operators and stabilizer operators.