The present study aimed to investigate the effects of increasing dietary lysine (Lys) levels with an adequate dietary crude protein (CP) content, as well as the effects of a reduction in dietary CP content with the recommended amino acid (AAs) level, on the performance, blood biochemical parameters, and histomorphology of the duodenum, liver, and kidney in broiler chickens. A total of 500 broiler chickens were randomly distributed into five dietary treatment groups, following a completely randomized design, where, at the beginning, the control group (C) was fed a diet containing the standard CP and Lys levels: 23% CP with 1.44% Lys during the starter period; 21.5% CP with 1.29% Lys during the growing period; and 19.5% CP with 1.16% Lys during the finishing period. The Lys content was increased by 10% above the recommended control basal requirements in the second group (Gr1) and by 20% in the third group (Gr2), while using the same recommended CP percentage as the C group. The fourth group (Gr3) had a 1% lower CP content and the fifth group had a 2% lower CP content than the C group, with the same recommended AA level as the C group. Increasing the Lys content in the Gr1 group improved the broilers’ weight gains (p < 0.05) during the starter, growing, and finishing periods. Decreasing dietary CP with the standard AA levels (Gr3 and Gr4) did not significantly affect (p > 0.05) the live weight gain, feed intake, or feed conversion ratio (FCR) of the broilers compared with those fed with the C diet. Blood total bilirubin, direct and indirect bilirubin, triglycerides, cholesterol, low-density lipoprotein (LDL), and very LDL were not different among the experimental groups. However, blood aspartate aminotransferase levels were increased (p < 0.05) in the Gr1 and Gr3 groups compared with the other treatment groups. All dietary treatments decreased the serum creatinine levels (p < 0.05) compared with the C group. The Gr2 broilers had greater serum total protein and globulin (p < 0.05) than those receiving the other treatments. Increasing dietary Lys levels resulted in a significant improvement in duodenum villus height and width (p < 0.05), while the low-CP diets resulted in shorter villi length and width, along with degenerated areas and lymphocytic infiltration. Low dietary CP content induced hepatocyte disorganization and moderate degeneration, along with vacuolated hepatic cells, excessive connective tissue, and lymphocytic infiltration. The cortical regions of the kidney exhibited obvious alterations in the Gr3 and Gr4 groups and large interstitial spaces were found between tubules. Renal tubules in the Gr3 and Gr4 groups were smaller in size and some of these tubules were atrophied. In conclusion, reducing dietary CP levels to 1% or 2% lower than the recommended level did not negatively affect growth performance, inducing minimal influence on the blood metabolic indicators of health status, and resulting in moderate alterations to the histomorphology of the duodenum, liver, and kidney. Furthermore, increasing the Lys content by 10% above the recommended level improved the growth performance, health status, and histomorphology of the duodenum, liver, and kidney in broiler chickens.