This feeding study investigated the hypothesis that over-processing of meat and bone meal (MBM) would impair the performance, gut health and ileal digestibility of nutrients in birds challenged with necrotic enteritis (NE). The effect of phytase (500 vs. 5,000 FTU/kg) was also examined using manufacturers recommended matrix values for 500 FTU for both levels. Ross 308 male broilers (
n
= 768) were assigned to 8 diets, with 6 replicate pens per diet and 16 birds per replicate pen using a randomized design with a factorial arrangement of treatments. Factors were NE challenge (no or yes), MBM (as received or over-processed), and phytase level (500 or 5,000 FTU/kg). Half of the birds were challenged with 5,000 oocysts of field strains of
Eimeria acervulina
and
Eimeria brunetti
, and 2,500 oocysts of
Eimeria maxima
on d 9 and 10
8
CFU/mL of
Clostridium perfringens
strain EHE-NE18 on d 14 and 15 post-hatch. Challenge × MBM interactions were detected for weight gain (WG), feed conversion ratio (FCR) and feed intake (FI) at d 14, 21 and 28, showing that challenged birds fed over-processed MBM had decreased WG (
P
< 0.05) and FI (
P
< 0.05) at d 14, increased FCR (
P
< 0.05) at d 21 and decreased WG (
P
< 0.05) and FI (
P
> 0.05) at d 28. Birds fed low phytase had increased livability (
P
< 0.05) at d 42. The challenge increased the prevalence and severity of NE induced lesions in the jejunum (
P
< 0.05) and ileum (
P
< 0.05). The birds fed over-processed MBM had decreased pH in the jejunum (
P
< 0.05) and ileum (
P
< 0.05) at d 16. High phytase increased apparent ileal digestibility (AID) of Ca (
P
< 0.05) and P (
P
< 0.05), and over-processed MBM increased AID of carbon (C;
P
< 0.05) and Ca (
P
< 0.05) at d 29. The challenge increased the caecal counts of
Lactobacillus
spp. (
P
< 0.05) and
C. perfringens
(
P
< 0.05) at d 16. The results indicated that supplementation of diets with high phytase reduces the negative impact on performance from over-processed MBM during NE as a result of increased nutrient digestibility.