Magic state distillation is one of the leading candidates for implementing universal faulttolerant logical gates. However, the distillation circuits themselves are not fault-tolerant, so there is additional cost to first implement encoded Clifford gates with negligible error. In this paper we present a scheme to faulttolerantly and directly prepare magic states using flag qubits. One of these schemes requires only three ancilla qubits, even with noisy Clifford gates. We compare the physical qubit and gate cost of our scheme to the magic state distillation protocol of Meier, Eastin, and Knill (MEK), which is efficient and uses a small stabilizer circuit. For low enough noise rates, we show that in some regimes the overhead can be improved by several orders of magnitude compared to the MEK scheme which uses Clifford operations encoded in the codes considered in this work.