Winter mortality is a common problem for Arkansas baitfish farmers that produce Fathead Minnow (FHM) Pimephales promelas and Golden Shiners (GS) Notemigonus crysoleucas. Winter feeding programs are a potential avenue to improve survival and condition and reduce weight loss of baitfish. Methods of winter feeding vary widely among producers, and currently there are no recognized best management practices. The impacts of different winter feeding regimens on FHM and GS survival, growth, and lipid storage were evaluated in temperature‐controlled aquarium systems. Fathead Minnow (mean ± SD = 0.88 ± 0.04 g) or GS (0.88 ± 0.02 g) were stocked at ambient water temperature, and the temperature was reduced to 6°C (FHM) or 8°C (GS) to mimic winter conditions. Three feeding regimens were implemented (3 tanks/regimen) that included ad libitum feeding twice per week (2×/week), once per week (1×/week), or once per month (1×/month). Significant differences in weight gain (loss), condition factor (K), and specific growth rate were observed after 13 weeks for FHM. Fish that were fed 2×/week gained nearly 3%, while fish that were fed 1×/week or 1×/month lost weight (2.3% and 10.1%, respectively). There were no significant differences in GS final weight (0.79–0.82 g), survival (65.0–88.3%), or weight gain (−6.84% to −9.50%) among treatments after 12 weeks. The GS from the 2×/week treatment had significantly higher K‐values than GS that were fed 1×/week or 1×/month. Fatty acid profiles of both species differed among treatments, showing a decline in saturated fatty acids from initial levels and an increase in polyunsaturated fatty acids (PUFAs) as feeding frequency decreased. Results suggest that fish may lose weight during the winter, but it does not appear to adversely affect survival, and both species alter their fatty acid compositions to optimize n‐3 PUFAs during cold water temperatures.