Traditional complementary foods are mainly starchy foods with limiting nutrient quality and can be fortified using protein rich crops like almond seed. This research thus aimed at investigating the nutritional quality of the formulated complementary diet from locally available almond seeds (Prunus amygdalus), high quality protein (QPM) and yellow maize after blending into flours. The proximate and amino acid compositions, in vitro protein qualities and functional properties of the blended flours were determined using standard methods. The in vivo studies involved feeding the weanling Wister albino rats with blended flours and commercial Cerelac (control), followed by hematological and histopathological determinations, while sensory attributes were evaluated by the semi-trained panelists. The protein contents of the flour blends (24–28%) were significantly (p < 0.05) better with adequate indispensable amino acids and improved functionalities than commercial cerelac (23%). Comparatively, the dried germinated QPM (DGQPM) has significant (p < 0.05) higher biological value (~ 37%) than fermented high QPM (FHQPM) (~ 30%), thereby indicating that the germination process improved protein quality of the diets. Besides, the in vivo data showed a positive effect of germination process as the rats fed with DGQPM has low white blood cells (30 × 102) compared to FHQPM (42 × 102) and cerelac (51 × 102). However, the fermentation process improved the packed cell volume of rats fed with FHQPM (49%) when compared to DGQPM and cerelac (47%). The formulated diets have no negative effects on the protein content (45.19–51.88 mg N/g) and weight (0.25–1.36 g) of the internal organs (liver, kidney and tissue) of the animals when compared to cerelac (53.72–55.04 mg N/g; 0.25–1.98 g), respectively. The panelists generally accepted all the formulated diets, hence encouraging their utilization in the global preparation of complimentary foods for young children to meet their nutritional needs and adding value to the locally produced underutilized almond seeds.