Chlorine‐based solutions are commonly used to sanitize orange fruits prior to juice extraction. We used flow cytometry (
FCM
) to investigate the physiology of
Escherichia coli
following its subjection to chlorine‐based solutions and alternative sanitizing agents (H
2
O
2
and organic acids). Green fluorescent protein (
GFP
)‐generating
E. coli
K‐12 were washed with 50–200 ppm available chlorine (
AC
), 1%–5% H
2
O
2
, 2%–4% citric acid, 4% acetic acid, or 4% lactic acid, after which they were added to 1.2 μm‐filtered orange juice (
OJ
). Cell physiology was investigated with
FCM
during storage at 4°C, and culturability was determined using plate counting. Analysis of
GFP
fluorescence allowed estimation of intracellular
pH
(
pH
i
).
FCM
results demonstrated an inverse relationship between the concentration of
AC
or H
2
O
2
and cellular health in
OJ
. Higher concentrations of sanitizer also resulted in a significantly greater number of viable but nonculturable (
VBNC
) cells. Real‐time
FCM
showed that supplementation of
AC
with 2% citric acid, but not with 100 ppm of Tween‐80, led to a significant reduction in
pH
i
of the cells incubated in
OJ
, and that the majority of the reduction in
pH
i
occurred during the first 2 min of incubation in
OJ
. Organic acids were found to be more effective than both
AC
and H
2
O
2
in reducing the
pH
i
, viability, and culturability of the cells in
OJ
. The results confirmed the hypothesis that consecutive subjection of
E. coli
to maximum legally permitted concentrations of sanitizers and
OJ
induces the
VBNC
state. Furthermore, we demonstrate successful application of
FCM
for monitoring the efficacy of washing procedures.