2019 Earnings UpdateFebruary 25, 2020

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2

Important Information about this Presentation

Forward-Looking Statements

Certain statements in this presentation constitute “forward-looking” statements. These statements are based on management’s current opinions,expectations, beliefs, plans, objectives, assumptions or projections regarding future events or future results. These forward-looking statements areonly predictions, not historical fact, and involve certain risks and uncertainties, as well as assumptions. Actual results, levels of activity,performance, achievements and events could differ materially from those stated, anticipated or implied by such forward-looking statements. WhileFreshpet believes that its assumptions are reasonable, it is very difficult to predict the impact of known factors, and, of course, it is impossible toanticipate all factors that could affect actual results. There are many risks and uncertainties that could cause actual results to differ materially fromforward-looking statements made herein, including, most prominently, the risks discussed under the heading “Risk Factors” in the Company’slatest annual report on Form 10-K filed with the Securities and Exchange Commission. Such forward-looking statements are made only as of thedate of this presentation. Freshpet undertakes no obligation to publicly update or revise any forward-looking statement because of newinformation, future events or otherwise, except as otherwise required by law. If we do update one or more forward-looking statements, noinference should be made that we will make additional updates with respect to those or other forward-looking statements.

Non-GAAP Measures

Freshpet uses certain non-GAAP financial measures, including EBITDA, Adjusted EBITDA, Adjusted EBITDA as a % of net sales, Adjusted GrossProfit, Adjusted Gross Profit as a % of net sales (Adjusted Gross Margin), Adjusted SG&A and Adjusted SG&A as a % of net sales. These non-GAAP financial measures should be considered as supplements to GAAP reported measures, should not be considered replacements for, orsuperior to, GAAP measures and may not be comparable to similarly named measures used by other companies.

Freshpet defines EBITDA as net income (loss) plus interest expense, income tax expense and depreciation and amortization expense. AdjustedEBITDA represents EBITDA plus loss on disposal of equipment, plant start-up expenses, non-cash share-based compensation, warrant fairvaluation, launch expense, fees related to secondary offerings, leadership transition expenses and litigation expense.

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Important Information about this Presentation (cont.)

Freshpet defines Adjusted Gross Profit as gross profit before non-cash depreciation expenses, plant start-up expenses and non-cash share-basedcompensation, and Adjusted SG&A as SG&A expenses before depreciation and amortization expense, non-cash share-based compensation, losson disposal of equipment, launch expense, fees related to secondary offerings, leadership transition expenses and litigation expense.

Management believes that the non-GAAP financial measures are meaningful to investors because they provide a view of the Company withrespect to ongoing operating results. Non-GAAP financial measures are shown as supplemental disclosures in this presentation because they arewidely used by the investment community for analysis and comparative evaluation. They also provide additional metrics to evaluate theCompany’s operations and, when considered with both the Company’s GAAP results and the reconciliation to the most comparable GAAPmeasures, provide a more complete understanding of the Company’s business than could be obtained absent this disclosure. The non-GAAPmeasures are not and should not be considered an alternative to the most comparable GAAP measures or any other figure calculated inaccordance with GAAP, or as an indicator of operating performance. The Company’s calculation of the non-GAAP financial measures may differfrom methods used by other companies. Management believes that the non-GAAP measures are important to an understanding of the Company’soverall operating results in the periods presented. The non-GAAP financial measures are not recognized in accordance with GAAP and should notbe viewed as an alternative to GAAP measures of performance.

See the Appendix hereto for a reconciliation of historical non-GAAP measures to the closest comparable GAAP measures. Certain non-GAAPmeasures present the Company’s guidance for fiscal year 2020. The Company does not provide guidance for the most directly comparable GAAPmeasure and similarly cannot provide a reconciliation to such measure without unreasonable effort due to the unavailability of reliable estimatesfor certain items. These items are not within the Company’s control and may vary greatly between periods and could significantly impact futurefinancial results.

7 of last 8 quarters >25%

growth

Q4 2019: Continued strong top line growth and accelerating bottom line

$51.6

$65.8

$9.2

$13.2

$7.0

$8.0

$9.0

$10.0

$11.0

$12.0

$13.0

$14.0

$15.0

$16.0

$17.0

$25.0

$30.0

$35.0

$40.0

$45.0

$50.0

$55.0

$60.0

$65.0

$70.0

$75.0

Q4 2018 Q4 2019

Freshpet Net Sales & Profitability Performance

Net Sales ($ millions) Adj. EBITDA ($ millions)

+30%

+27%

+34%

+43%

4

Net Income (Loss) ($ millions)

$4.6$1.8

5

Exceeded guidance:

Net Sales:>$244M

Adj. EBITDA: >$29M

FY 2019: Continued strong top line growth and accelerating bottom line

$152.4

$193.2

$245.9

$17.6

$20.3

$29.2

$15.0

$17.0

$19.0

$21.0

$23.0

$25.0

$27.0

$29.0

$31.0

$33.0

$100.0

$120.0

$140.0

$160.0

$180.0

$200.0

$220.0

$240.0

$260.0

2017 2018 2019

Freshpet Net Sales & Adj. EBITDA Performance

Net Sales ($ millions) Adj. EBITDA ($ millions)

+27%

+27%

+17%+15%

+44%

-1%

($4.3) ($5.4) ($1.4)

Net Income (Loss) ($ millions)

15.3%

17.4%

19.3%20.1%

21.8%

23.7%22.7%22.3%

21.8%

20.4%

23.3%

22.0%

23.6%24.1%

24.8%25.1%

27.0%26.6%

28.1%

31.0%30.3%30.0%

31.9%

30.1%30.1%

27.4%27.2%27.7%

29.5%29.2%

27.0%26.0 25.925.8%

23.924.0%

25.4%

27.8%27.1%

29.0%

8.2%7.8%

6.3%5.8%6.0%6.1%5.7%

6.4%6.4%6.4%6.6%6.5%6.4%6.1%6.6%

7.2%7.6%7.6%7.3%7.2%6.6%6.7%6.9%6.8%6.5%6.1%6.4%6.3%

7.5%8.1 8.3%8.6%8.8%

9.4%10.0%

9.5%9.6%

11.7%

14.8%14.9%

Nielsen Mega-Channel Consumption and Distribution Growth

Dollar Sales % Chg YA ACV % chg YAGO Dollar Sales

6

>20% Growth Every Period Since

March 2017

Accelerating Consumption Growth and Strong Distribution Growth

Source: Nielsen Mega-Channel Data thru 1/25/20

Sustainable and predictable

business model

Growth rates continue to build

21.8 21.6 23.0 24.927.7

30.8 29.3 28.0 27.1 25.0 26.6 27.8

36.6 37.841.8

47.2

55.559.1 59.0 59.9 62.2 63.5 63.7 64.0

13

wk

% C

han

ge

Freshpet RFG YoY Change – Mega-Channel

% Chg vs. YAG % Chg vs.2 YAG

8

Two-year stacked growth of 56% in

Nielsen Mega-Channel

Q4 2019: Strong growth across channels

27%

31%34%

9%

0%

5%

10%

15%

20%

25%

30%

35%

40%

Mega-Channel XAOC Food Big Box Pet

Q4 2019 Nielsen Consumption Growth

Source: Nielsen Consumption Data thru 12/28/19

9

Second year of at least 27% Nielsen

Mega-Channel growth

FY 2019: Strong growth across channels

27%30%

35%

13%

0%

5%

10%

15%

20%

25%

30%

35%

40%

Mega-Channel XAOC Food Big Box Pet

CY 2019 Nielsen Measured Consumption Growth

Source: Nielsen Consumption Data thru 12/28/19

10

15% increase in ACV in 2019

Accelerating % ACV growth

43.143.5

43.944.2 44.5 44.6 44.8 45.0 45.2 45.4 45.6 45.6 45.6

45.946.2

47.247.8

48.1 48.448.8

49.249.6 49.7

50.0

50.9

52.3

52.7

42.0

44.0

46.0

48.0

50.0

52.0

54.0

Freshpet % ACV

Source: Nielsen Mega-Channel Data thru 1/25/20

11

16% increase in TDP’s in 2019

Increasing Total Distribution Points (TDP’s)

475.0

525.0

575.0

625.0

675.0

725.0

775.0

4 W

/E 1

1/0

5/1

6

4 W

/E 1

2/0

3/1

6

4 W

/E 1

2/3

1/1

6

4 W

/E 0

1/2

8/1

7

4 W

/E 0

2/2

5/1

7

4 W

/E 0

3/2

5/1

7

4 W

/E 0

4/2

2/1

7

4 W

/E 0

5/2

0/1

7

4 W

/E 0

6/1

7/1

7

4 W

/E 0

7/1

5/1

7

4 W

/E 0

8/1

2/1

7

4 W

/E 0

9/0

9/1

7

4 W

/E 1

0/0

7/1

7

4 W

/E 1

1/0

4/1

7

4 W

/E 1

2/0

2/1

7

4 W

/E 1

2/3

0/1

7

4 W

/E 0

1/2

7/1

8

4 W

/E 0

2/2

4/1

8

4 W

/E 0

3/2

4/1

8

4 W

/E 0

4/2

1/1

8

4 W

/E 0

5/1

9/1

8

4 W

/E 0

6/1

6/1

8

4 W

/E 0

7/1

4/1

8

4 W

/E 0

8/1

1/1

8

4 W

/E 0

9/0

8/1

8

4 W

/E 1

0/0

6/1

8

4 W

/E 1

1/0

3/1

8

4 W

/E 1

2/0

1/1

8

4 W

/E 1

2/2

9/1

8

4 W

/E 0

1/2

6/1

9

4 W

/E 0

2/2

3/1

9

4 W

/E 0

3/2

3/1

9

4 W

/E 0

4/2

0/1

9

4 W

/E 0

5/1

8/1

9

4 W

/E 0

6/1

5/1

9

4 W

/E 0

7/1

3/1

9

4 W

/E 0

8/1

0/1

9

4 W

/E 0

9/0

7/1

9

4 W

/E 1

0/0

5/1

9

4 W

/E 1

1/0

2/1

9

4 W

/E 1

1/3

0/1

9

4 W

/E 1

2/2

8/1

9

4 W

/E 1

/25

/20

Freshpet Total Distribution Points (TDP)Nielsen Mega-Channel

Source: Nielsen Mega-Channel Data thru 1/25/20

12

Almost Doubled Core Dog HH Penetration in

3 Years

Accelerating Penetration Growth

Source: Nielsen HH Panel for the period ending Dec 2019

1.50 1.56

1.75

2.04

2.54

0.98 1.031.14

1.51

1.97

0.75

0.95

1.15

1.35

1.55

1.75

1.95

2.15

2.35

2.55

2.75

2015 2016 2017 2018 2019

Freshpet Penetration Growth

Total Penetration (%) Core Dog Penetration (%)

Total Penetration Trendline Core Dog Penetration Trendline

+32%

+11%

+30%

+25%

+5%

+17%

+12%

+4%

13

18% Increase in Core Dog Buying Rate Since 2015

Buying Rate Growth Diluted by Strong Penetration Growth

$83.17

$90.29

$96.53

$105.78 $106.65$105.24

$113.55

$125.88 $125.89 $124.35

$60.00

$70.00

$80.00

$90.00

$100.00

$110.00

$120.00

$130.00

$140.00

2015 2016 2017 2018 2019

Freshpet Buying Rate

Total Buying Rate Core Dog Buying Rate

Source: Nielsen HH Panel for the period ending Dec 2019 and company internal data

14

2,071 Net New Stores in 2019

Increasing Freshpet Store Count

10,826

13,387

15,015

16,609

18,004

19,499

21,570

10,000

12,000

14,000

16,000

18,000

20,000

22,000

24,000

2013 2014 2015 2016 2017 2018 2019

+11%

+8%

+8%

+11%

+12%

+24%

+28%

Source: Internal company data

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Q4 2019: Stable Gross Margins

50.4%48.5%

49.8% 49.1%

Q1 2019 Q2 2019 Q3 2019 Q4 2019

Freshpet Adj. Gross Margin Progress

~50% Adj. Gross Margin Provides

Adequate Resources for

Marketing Investment

47.3%45.5%

47.0%46.0%

Q1 2019 Q2 2019 Q3 2019 Q4 2019

Freshpet Gross Margin Progress

16

FY 2019: Stable Gross Margins

50.2% 49.4%

2018 2019

Freshpet Adj. Gross Margin Progress

Stable Gross Margin Despite Challenges of Rapid Growth

46.6% 46.4%

2018 2019

Freshpet Gross Margin Progress

17

Gained 150 bps of Adj. SG&A (excl. media) leverage

Q4 2019: Continued gains in SG&A leverage

27.7%

26.3%

31.5%

29.3%

Q4 2018 Q4 2019

Adj. SG&A Leverage Progress – Q4 2019

Adj. SG&A % Excluding Media

Total Adj. SG&A %

Media: 3.7%

Media: 3.0%

41.6%

38.6%

Q4 2018 Q4 2019

SG&A Leverage Progress – Q4 2019

Total Adj. SG&A %

18

Gained 290 bps of Adj. SG&A (excl. media) Leverage

FY 2019: Continued Gains in SG&A Leverage

28.5%

25.6%

39.7%37.6%

FY 2018 FY 2019

Adj. SG& Leverage Progress -- CY 2019

Adj. SG&A % Excluding Media Total Adj. SG&A %

Media: 11.1% Media:

12.0%

49.1%46.6%

FY 2018 FY 2019

SG& Leverage Progress -- CY 2019

Total SG&A %

19

2020 Goal: 700 bps of Adjusted

SG&A (excl. media) leverage

Captured 560 bps of Adjusted SG&A (excl. Media) leverage since 2016

$129.7 $152.4

$193.2

$245.9 31.2% 31.0%

28.5%

25.6%

20.0%

22.0%

24.0%

26.0%

28.0%

30.0%

32.0%

$0.0

$50.0

$100.0

$150.0

$200.0

$250.0

$300.0

2016 2017 2018 2019

Adj. SG&A Excluding Media Leverage Progress

Net Sales (millions)

Adj. SG&A (excluding media)

$129.7 $152.4

$193.2

$245.9 48.3% 49.3%49.1%

46.6%

20.0%

25.0%

30.0%

35.0%

40.0%

45.0%

50.0%

55.0%

$0.0

$50.0

$100.0

$150.0

$200.0

$250.0

$300.0

2016 2017 2018 2019

SG&A Leverage Progress

Net Sales (millions)

SG&A

20

Original 2020 “Feed the Growth”

Net Sales Goal: $300 Million

On Track to Exceed 2020 Net Sales Goal

$129.7$152.4

$193.2

$245.9

$300.0

$0.0

$50.0

$100.0

$150.0

$200.0

$250.0

$300.0

$350.0

2016 2017 2018 2019 2020 Goal

Progress Towards Original 2020 “Feed The Growth” Net Sales Goal

+14%+18%

+27%

+27%

+22%

+22%

21

Accelerated Growth Rate and Beginning

to Capture Scale Benefits

“Feed the Growth” is Working

Reconciliation of gross profit to adjusted gross profit

29

Three Months Ended Twelve Months Ended

December 31, December 31,

2019 2018 2019 2018

(Dollars in thousands) (Dollars in thousands)

Gross Profit $ 30,250 $ 23,368 $ 114,197 $ 89,990

Depreciation expense (a) 1,616 1,520 6,370 6,089

Plant start-up expense (b) — — — —

Non-cash share-based compensation (c) 414 635 922 859

Adjusted Gross Profit $ 32,279 $ 25,523 $ 121,489 $ 96,938

Adjusted Gross Profit as a % of Net Sales 49.1 % 49.4 % 49.4 % 50.2 %

(a) Represents depreciation and amortization expense included in cost of goods sold. (b) Represents additional operating costs incurred in connection with the start-up of our new manufacturing lines as part

of the Freshpet Kitchens expansion project in 2016 that included adding two additional product lines.

(c) Represents non-cash share-based compensation expense included in cost of goods sold.

Reconciliation of SG&A expenses to adjusted SG&A expenses

30

Three Months Ended Twelve Months Ended

December 31, December 31,

2019 2018 2019 2018

(Dollars in thousands) (Dollars in thousands)

SG&A expenses $ 25,375 $ 21,478 $ 114,450 $ 94,876

Depreciation and amortization expense (a) 2,598 2,127 9,551 7,977

Non-cash share-based compensation (b) 1,714 2,002 6,912 5,949

Launch expense (c) 1,228 863 4,563 3,540

Loss on disposal of equipment 649 649 —

Secondary offering expenses (d) (47 ) 225 302 362

Leadership transition expenses (e) — — — —

Litigation expense (f) — — — 348

Adjusted SG&A Expenses $ 19,233 $ 16,261 $ 92,473 $ 76,698

Adjusted SG&A Expenses as a % of Net Sales 29.3 % 31.5 % 37.6 % 39.7 %

(a) Represents depreciation and amortization expense included in SG&A. (b) Represents non-cash share-based compensation expense included in SG&A. (c) Represents new store marketing allowance of $1,000 for each store added to our distribution network, as well as the

non-capitalized freight costs associated with Freshpet Fridge replacements. The expense enhances the overall marketing spend to support our growing distribution network.

(d) Represents fees associated with secondary public offerings of our common stock. (e) Represents charges associated with our former Chief Executive Officer’s separation agreement, as well as changes

in estimates associated with leadership transition costs. (f) Represents fees associated with two securities lawsuits.

Reconciliation of net income to adjusted EBITDA

31

Exhibit 99.1 Three Months Ended Twelve Months Ended

December 31, December 31,

2019 2018 2019 2018

(Dollars in thousands) (Dollars in thousands)

Net income (loss) 4,633 $ 1,757 $ (1,383 ) $ (5,361 )

Depreciation and amortization 4,214 3,649 15,921 14,068

Interest expense 302 35 991 296

Income tax expense 87 20 144 77

EBITDA $ 9,236 $ 5,461 $ 15,673 $ 9,080

Loss on disposal of equipment 649 37 787 142

Non-cash share-based compensation 2,128 2,637 7,834 6,808

Launch expense (a) 1,228 863 4,563 3,540

Plant start-up expenses (b) — — — —

Warrant fair valuation (c) — — — —

Secondary offering expenses (d) (47 ) 225 302 362

Leadership transition expenses (e) — — — —

Litigation expense (f) — — — 348

Adjusted EBITDA $ 13,194 $ 9,223 $ 29,159 $ 20,280

Adjusted EBITDA as a % of Net Sales 20.1 % 17.9 % 11.9 % 10.5 %

(a) Represents new store marketing allowance of $1,000 for each store added to our distribution network, as well as the

non-capitalized freight costs associated with Freshpet Fridge replacements. The expense enhances the overall

marketing spend to support our growing distribution network. (b) Represents additional operating costs incurred in connection with the start-up of our new manufacturing lines as part

of the Freshpet Kitchens expansion project in 2016 that included adding two additional product lines. (c) Represents the change of fair value for the outstanding common stock warrants. All outstanding warrants were

converted to common stock in September 2017. (d) Represents fees associated with secondary public offerings of our common stock.

(e) Represents charges associated with our former Chief Executive Officer’s separation agreement as well as changes in estimates associated with leadership transition costs.

(f) Represents fees associated with two securities lawsuits.