We propose BQTRU, a non-commutative NTRU-like cryptosystem over quaternion algebras. This cryptosystem uses bivariate polynomials as the underling ring. The multiplication operation in our cryptosystem can be performed with high speed using quaternions algebras over finite rings. As a consequence, the key generation and encryption process of our cryptosystem is faster than NTRU in comparable parameters. Typically using Strassen's method, the key generation and encryption process is approximately 16/7 times faster than NTRU for an equivalent parameter set. Moreover, the BQTRU lattice has a hybrid structure that makes inefficient standard lattice attacks on the private key. This entails a higher computational complexity for attackers providing the opportunity of having smaller key sizes. Consequently, in this sense, BQTRU is more resistant than NTRU against known attacks at an equivalent parameter set. Moreover, message protection is feasible through larger polynomials and this allows us to obtain the same security level as other NTRU-like cryptosystems but using lower dimensions.