We demonstrate that magnetic phase separation and competing spin order in the colossal magnetoresistive (CMR) manganites can be directly explored via tuning strain in bulk samples of nanocrystalline La$_{1-x}$Ca$_x$MnO$_3$. Our results show that strain can be reversibly frozen into the lattice in order to stabilize coexisting antiferromagnetic domains within the nominally ferromagnetic metallic state of La$_{5/8}$Ca$_{3/8}$MnO$_3$. The measurement of tunable phase separation via magnetic neutron powder diffraction presents a direct route of exploring the correlated spin properties of phase separated charge/magnetic order in highly strained CMR materials and opens a potential avenue for realizing intergrain spin tunnel junction networks with enhanced CMR behavior in a chemically homogeneous material.