Natural Cycles and Flo are both period-tracking apps, but they occupy fundamentally different categories. Natural Cycles is FDA-cleared as a contraceptive device, built around daily basal body temperature readings and a proprietary algorithm that identifies fertile and non-fertile days. Flo is primarily a menstrual calendar and health tracker that predicts upcoming periods and fertile windows based on cycle history, without the regulatory clearance to market itself as birth control. That distinction shapes almost everything about how the two apps work, how reliable they are, and what you should expect from each.
What Each App Actually Does
Natural Cycles asks you to take your temperature every morning before getting out of bed, ideally with a two-decimal-place basal thermometer. The app feeds that reading into an algorithm that, over time, learns your individual cycle pattern. Each day, you get a red day (potentially fertile, use protection or abstain) or a green day (low risk of pregnancy). The algorithm also incorporates optional luteinizing hormone test results for more precision. In the first few cycles, the app tends to be conservative, assigning more red days while it gathers data. By the twelfth cycle, users were seeing roughly 59% green days on average, with wrong green days averaging just 0.08% of the total.
Flo works differently. You log the start and end of your period, and the app uses that history to predict your next cycle start date and estimate a fertile window. You can also log symptoms like mood, discharge, cramps, and sleep. Flo’s predictions improve as it accumulates more cycle data, but they remain calendar-based estimates rather than real-time physiological measurements. This is a meaningful difference: a calendar method can tell you when ovulation probably happened based on past patterns, but it cannot confirm that ovulation is actually happening right now in this specific cycle.
The Temperature Signal Behind Natural Cycles
The biological foundation of Natural Cycles is the post-ovulation rise in basal body temperature. After you ovulate, progesterone levels climb, and your core temperature increases by about 0.3°C to 0.7°C compared to the first half of your cycle. This shift is most reliable when measured during sleep or immediately upon waking, before any physical activity. Natural Cycles uses this retrospective temperature shift to confirm that ovulation has occurred, then combines it with cycle-length data to predict when it will likely occur in future cycles.
Flo does not use temperature data in the same structured way. While you can log temperature in Flo, the app’s fertile window predictions are driven primarily by your period dates and cycle length history. Without a temperature-based confirmation of ovulation, Flo’s estimates are closer to what researchers call calendar-based methods, which assume ovulation happens at a predictable point in every cycle. For people with regular, clockwork cycles, that assumption works reasonably well. For people whose cycles vary by even a few days, it becomes less reliable.
What the Clinical Evidence Says About Effectiveness
Natural Cycles has published peer-reviewed effectiveness data, which is a prerequisite for its FDA clearance. A large prospective study found a perfect-use Pearl Index of 1.0 pregnancies per 100 woman-years and a typical-use Pearl Index of 6.9, corrected to 6.8 when limiting follow-up to 12 months. In plain terms, if 100 women used the app perfectly for a year, about 1 would become pregnant. Under typical use, where people occasionally have unprotected sex on red days, skip temperature measurements, or make other errors, about 7 out of 100 would become pregnant over a year.
A separate U.S. cohort study found broadly similar numbers: a 13-cycle cumulative pregnancy probability of 7.2% under typical use and a perfect-use Pearl Index of 2.0. The slightly higher perfect-use rate in this study compared to the European data likely reflects differences in how the study populations were recruited and followed, but the overall picture is consistent.
Flo has not published comparable contraceptive effectiveness data because it is not marketed or cleared as a contraceptive. This does not mean Flo is useless for understanding your cycle, but it does mean there is no peer-reviewed number you can point to and say “Flo prevents pregnancy at X rate.” If you are relying on any app specifically to avoid pregnancy, this distinction matters enormously. Using Flo’s fertile window estimate as your sole method of contraception is, from a clinical standpoint, using an unvalidated calendar method.
Why Your Previous Contraception Matters
One of the more surprising findings from Natural Cycles research is that your contraceptive history before switching to the app affects how well it works for you. A postmarket surveillance study of over 16,000 women found that those who had not recently used hormonal contraception had a typical-use Pearl Index of 5.1, while women coming off hormonal methods had a Pearl Index of 7.5. The gap was even more striking when broken down further: women who had previously used condoms did best, with a Pearl Index of 3.5, while women switching directly from the pill did worst, at 8.1.
The likely explanation is that hormonal contraception suppresses ovulation and can temporarily alter cycle patterns after discontinuation. Women coming off the pill often experience irregular cycles for several months, which makes it harder for any algorithm to accurately predict fertile windows. If you are switching to Natural Cycles from hormonal birth control, expect a longer learning period for the app and more red (caution) days early on. This is something Flo users would also experience in terms of less accurate predictions, though without the same structured research documenting the effect.
Wearable Devices and the Future of Temperature Tracking
One practical complaint about Natural Cycles has always been the daily ritual of taking your temperature with a basal thermometer the moment you wake up. If you forgot, slept badly, or got up to use the bathroom first, the reading could be unreliable. Wearable devices that measure skin temperature continuously during sleep aim to solve this problem, and Natural Cycles now integrates with wearable sensors.
Research comparing wrist-worn skin temperature sensors to traditional oral basal thermometry found that wrist temperature was more sensitive for detecting ovulation, with a sensitivity of 0.62 compared to 0.23 for BBT. However, that higher sensitivity came with a trade-off: the false-positive rate was also higher (8.8% versus 3.6%), meaning the wrist sensor sometimes flagged ovulation when it had not actually occurred. In practice, this means wearable-based tracking catches more true ovulations but also generates more noise, which the algorithm then has to filter out.
Flo has partnered with various wearable brands for general health tracking integration, but this is more about syncing step counts, sleep data, and heart rate than about feeding a clinically validated fertility algorithm. The data flows into Flo as supplementary information rather than as the backbone of a contraceptive method.
Privacy and What Happens to Your Data
Both apps collect deeply personal information: menstrual dates, sexual activity, symptoms, and in Natural Cycles’ case, daily temperature readings. Where that data goes is a legitimate concern, and the two apps have very different track records.
Flo faced a Federal Trade Commission complaint in 2020 for sharing sensitive user health data with third-party companies, including major advertising platforms, despite promising users that their information would be kept private. This was not a minor oversight: the FTC found that Flo disclosed health information like pregnancy status and period dates to analytics and marketing firms. The case highlighted a gap in how reproductive health apps are regulated in the United States, where most period trackers fall outside the scope of medical device regulation and therefore outside the stricter data protections that come with it.
A broader analysis of reproductive health apps’ privacy policies found that major concerns included the use of IP address tracking and the involvement of third parties for advertising and marketing, as well as the potential for data misuse. These problems are not unique to Flo; they reflect an industry-wide pattern where free apps monetize user data in ways that are buried in lengthy privacy policies most people never read.
Natural Cycles, because it is classified as a medical device, is subject to additional regulatory scrutiny. The company has marketed itself on privacy and states that it does not sell user data. That said, regulatory classification alone does not guarantee perfect data handling, and the broader conversation about reproductive health data has intensified considerably since 2022, when changes in U.S. abortion law made the potential consequences of data exposure more concrete for many users.
The Emotional Side of Cycle Tracking
Something that rarely comes up in app store reviews but shows up clearly in research is the psychological weight of cycle tracking. A survey of women using period tracker apps found that many felt worried, stressed, and even let down when their period arrived earlier than the app predicted. For women trying to conceive, an inaccurate prediction could trigger anxiety about ovulation timing. For women trying to avoid pregnancy, it could spark a pregnancy scare. The emotional response was tied directly to how much trust the user placed in the app’s predictions.
Research specifically on Natural Cycles users trying to conceive found that while the app was perceived as empowering and “natural,” it also intervened in daily life and relationships in ways users did not always anticipate. Temperature data became a focal point of morning routines and partner conversations. The technology sometimes privileged its own metrics over the user’s embodied knowledge of their own body, creating tension when the numbers did not match how someone felt. Researchers noted that this dynamic could reproduce gendered patterns where the burden of reproductive management falls disproportionately on one partner.
Flo users report similar experiences. The app’s prediction of a fertile window or upcoming period becomes a source of reassurance when accurate and a source of anxiety when wrong. Because Flo’s predictions are based on less precise data inputs than Natural Cycles, the margin for prediction error can be wider, which in turn can amplify the emotional swings that come with tracking.
When Neither App Works Well
Both Natural Cycles and Flo perform best for people with reasonably regular ovulatory cycles. If your cycles are irregular, the picture changes. A clinical consensus review noted that most self-monitoring fertility technologies rely on predictive algorithms developed in populations with regular ovulatory cycles, which limits their usefulness for people with conditions like polycystic ovary syndrome, where ovulation can be unpredictable, delayed, or absent in some cycles.
Natural Cycles addresses this partly by being conservative: if the algorithm cannot confidently identify a post-ovulation temperature shift, it assigns more red days. You lose green days, but the safety margin increases. Flo, however, will still display a predicted fertile window based on your historical cycle length, which may bear little resemblance to what your body is actually doing in a given cycle. For someone with PCOS tracking cycles that range from 25 to 60 days, Flo’s fertile window estimate is essentially a guess.
Shift workers, frequent travelers crossing time zones, and people with disrupted sleep patterns also face challenges. Basal body temperature is sensitive to sleep quality and timing, so Natural Cycles users who work nights or have inconsistent wake times may get unreliable readings. Wearable sensors help somewhat by measuring temperature continuously rather than at a single morning snapshot, but the underlying biological signal is still affected by sleep disruption. Flo’s calendar-based approach is not directly affected by sleep patterns, but it also does not gain any information from them.
Perimenopause and the Limits of Prediction
As women enter their forties and approach menopause, cycle patterns begin to shift. Cycles may become shorter or longer, ovulation may become sporadic, and hormone levels fluctuate more dramatically from month to month. A retrospective analysis of women aged 40 to 50 who tracked their cycles found that the perimenopausal period produced distinct hormonal cycle characteristics that differed markedly from younger reproductive-age patterns.
For Natural Cycles users in perimenopause, this means the algorithm may struggle to establish consistent patterns, leading to more red days and less certainty. The app was primarily studied in reproductive-age women, and its published effectiveness data does not specifically address perimenopausal users. For Flo users, cycle prediction accuracy tends to degrade as cycle variability increases, since the app’s predictions are anchored to historical averages that may no longer apply.
Neither app is designed to diagnose or manage menopause. They can, however, give you a useful longitudinal record of how your cycles are changing over time, which can be valuable information to bring to a healthcare provider. In that sense, both apps function well as tracking tools even when their predictive accuracy diminishes.
Cost and Accessibility
Natural Cycles requires a paid subscription, typically around $100 per year or a monthly fee, and the company sells its own basal thermometer as a companion product. Wearable integration (using a compatible smart ring or wristband) adds the cost of that device. The subscription model reflects the app’s positioning as a medical device with ongoing algorithmic support and regulatory obligations.
Flo offers a free tier that covers basic period tracking and predictions. A premium subscription unlocks additional features like health insights, guided courses, and personalized content. The free version is functional enough for straightforward cycle tracking, which is a significant accessibility advantage. For someone who simply wants to know when their period is likely to arrive, Flo’s free tier does the job without requiring any additional hardware.
The cost difference reflects the fundamental divide between the two products. You are paying Natural Cycles for a clinically validated contraceptive algorithm backed by peer-reviewed data. You are paying Flo for a polished health and wellness platform with extensive content. Neither price is unreasonable for what it delivers, but confusing the two products’ purposes can lead to real consequences. Using a wellness tracker as birth control, or expecting a contraceptive app to serve as a comprehensive health companion, means misunderstanding what you bought.
Choosing Between Them
If your primary goal is contraception without hormones, Natural Cycles is the only one of the two with clinical data and regulatory clearance to back that claim. Its effectiveness under typical use sits in the range of about 6 to 7 pregnancies per 100 woman-years across multiple studies, which places it roughly between condoms and hormonal methods like the pill in real-world performance. You need to be willing to take your temperature consistently, abstain or use barrier methods on red days, and accept that the first few cycles will involve more caution days as the algorithm learns your pattern.
If your goal is general cycle awareness, symptom logging, or simply knowing when your period is coming, Flo is a capable and accessible option. Its predictions improve with consistent use, and its interface is designed around a broad wellness experience rather than a narrow contraceptive function. Just keep in mind that Flo’s fertile window estimates are not validated for pregnancy prevention, and its data privacy practices have historically drawn scrutiny.
Some people use both: Natural Cycles for its contraceptive algorithm and Flo for its symptom tracking and community features. There is nothing wrong with that approach, as long as contraceptive decisions are based on the app with the evidence behind it. The worst outcome is treating two very different tools as interchangeable because they both have a calendar icon and a pink color scheme.