Higher-protein diets, meal replacements, and greater early weight loss have separately been associated with greater weight loss. We compared a high-protein, meal replacement program with daily energy restriction (DER) to one which provided greater energy restriction adding alternate day fasting (ADF + DER; alternating days of modified-fasting and DER plus 1 ad libitum day/week) on retention, weight loss, physiological, nutritional, and behavioral markers. Participants were randomized to ADF + DER or DER for 16 weeks (n = 162, age 40 ± 8 years BMI 36 ± 6 kg/m2 (Mean ± SD)) plus 8 weeks weight maintenance. At week 16 weight change was −10.7 ± 0.5 kg and −11.2 ± 0.6 kg in ADF + DER and DER groups (treatment NS). Fat mass, visceral adipose tissue, and lean mass (p < 0.05) were similarly reduced between treatments. Weight loss was sustained to 24 weeks (treatment NS). Fasting LDL-cholesterol, triglycerides, insulin, hsCRP, glucose, and blood pressure all improved (p < 0.05; treatment NS). Transferrin saturation, ferritin, serum zinc, folate, and B12 improved (p < 0.05; treatment NS). Plasma thiamine and vitamin D levels decreased, reflecting lower carbohydrate intakes and seasonal changes, respectively. Food cravings, quality of life, and mood improved (treatment NS). Energy, fatigue, and pain improved slightly more in DER (p < 0.05). This study supports the use of higher protein, meal replacement programs with or without ADF in weight management.