We have previously shown protein-polyphenol drinks consumed post-exercise and before bed accelerate functional recovery following eccentric contractions (EC). Microarray analysis has identified the inflammatory NF-kB signalling pathway as important 3 h after EC, but its involvement beyond 3 h and association with functional recovery of skeletal muscle is unclear. Here we investigate changes in NF-kB associated transcripts and muscle force production for 168h following EC and the effect of protein-polyphenol drink consumption. In a randomised, parallel groups, placebo controlled double blind design, eighteen healthy males and females (22 ± 1 y; BMI: 24.0 ± 0.9 kg/m2 (± SEM)) consumed a controlled isocaloric diet (1.2 g/kg protein) for 6 days before and 7 after a single bout of 300 maximal unilateral quadriceps EC, in combination with either daily post-exercise (20 g whey, casein and pea protein blend and 650 mg pomegranate extract) and pre-bed (20 g casein protein and 480 mg tart cherry extract) drinks (Beachbody LLC) (PRO; n = 9; 4 females), or isocaloric maltodextrin placebos (PLA; n = 9; 3 females). Total isokinetic work over 30 maximal knee extensions (TW) was measured relative to the contralateral control leg (%con) before and every 24 h for 7 d following EC. Muscle biopsies from the vastus lateralis were taken 24, 27, 36, 72 and 168 h post EC. RT-PCR of 21 NF-kB related transcripts was performed using OpenArray plates on a QuantStudio 12K Flex System. Data were normalised to α-actin and β2-microglobulin, and the control leg of a PLA subject, using the 2-(ΔΔCt) method. Muscle function and gene expression data were analysed using two- (group*time) and three-way (leg*group*time) ANOVAs, respectively. EC caused a maximum decline in TW after 48 h in PLA to 68 ± 6 %con (P<0.001), which remained impaired until 120 h. Conversely, TW in PRO was impaired at 24 h only (89 ± 5 %con; P<0.05). We identified 10 differentially expressed NF-kB associated transcripts in the eccentric leg 24 – 168 h post EC (P<0.05). Of these, 8 showed an increase in expression at 24 h in both groups, 2 in PLA only (IL1R1, IL1RL1) and 1 in PRO only (NFKB1) (P<0.05). Interaction effects show the expression of two cytokine receptors, IL1R1 and IL1RL1 peaked at 24 h in PLA (16.8 ± 4.7 fold and 216.0 ± 96.3 fold, respectively. P<0.01) and declined linearly thereafter. Expression of both IL1R1 and IL1RL1 was higher in PLA than PRO at 24 h (PRO = 5.5 ± 8.6 and 38.4 ± 23.5 fold, respectively. P<0.05). IL1R1 and IL1RL1 expression in PRO did not change throughout the time course. Increased expression of some NF-kB related transcripts precedes the functional decline of skeletal muscle following EC. Post-exercise and before bed protein-polyphenol beverages attenuate this response suggesting inflammatory NF-kB signalling may negatively impact recovery following EC.