We construct the gravity dual of three-dimensional, $SU(N_{\textrm{c}})$super Yang-Mills theory with $N_{\textrm{f}}$ flavors of dynamical quarks inthe presence of a non-zero quark density $N_{\textrm{q}}$. The supergravitysolutions include the backreaction of $N_{\textrm{c}}$ color D2-branes and$N_{\textrm{f}}$ flavor D6-branes with $N_{\textrm{q}}$ units of electric fluxon their worldvolume. For massless quarks, the solutions depend non-triviallyonly on the dimensionless combination $\rho=N_{\textrm{c}}^2 N_{\textrm{q}} /\lambda^2 N_{\textrm{f}}^4$, with $\lambda=g_{\textrm{YM}}^2 N_{\textrm{c}}$the 't Hooft coupling, and describe renormalization group flows between thesuper Yang-Mills theory in the ultraviolet and a non-relativistic theory in theinfrared. The latter is dual to a hyperscaling-violating, Lifshitz-likegeometry with dynamical and hyperscaling-violating exponents $z=5$ and$\theta=1$, respectively. If $\rho \ll 1$ then at intermediate energies thereis also an approximate AdS$_4$ region, dual to a conformal Chern-Simons-Mattertheory, in which the flow exhibits quasi-conformal dynamics. At zerotemperature we compute the chemical potential and the equation of state andextract the speed of sound. At low temperature we compute the entropy densityand extract the number of low-energy degrees of freedom. For quarks of non-zeromass $M_{\textrm{q}}$ the physics depends non-trivially on $\rho$ and$M_{\textrm{q}} N_{\textrm{c}}/\lambda N_{\textrm{f}}$.