Semimagnetic Pb1-xMnxSe nanocrystals were synthesized by a fusion method in a glass matrix and characterized by optical absorption (OA), atomic/magnetic force microscopy (AFM/MFM), and photoluminescence techniques. MFM images strongly indicated the formation of Pb1-xMnxSe magnetic phases in the glass system. Quantum dot size was manipulated by tuning annealing time. It was shown that Mn2+ impurity affects nucleation, where Mn2+-doped samples present a redshift of the OA peak after a short annealing time and a blueshift after long annealing time compared to undoped PbSe NCs. This behavior was linked to the dependence of band-gap energy and the absorption selection rule on Mn2+ concentration. Photoluminescence in the Pb1-xMnxSe nanocrystals increases as the temperature rises up to a point and then decreases at higher temperatures. Anomalous increases in emission efficiency were analyzed by considering temperature induced carrier-transfer in semimagnetic Pb1-xMnxSe quantum dots nanocrystals of different sizes.